bluuebunny/crossref_metadata_2025 huggingface dataset:
CryoEM structure and assembly mechanism of a bacterial virus genome gatekeeper
Authors: Orlov Igor , Roche Stéphane , Brasilès Sandrine , Lukoyanova Natalya , Vaney Marie-Christine , Tavares Paulo , Orlova Elena V.
Published: November 2022

Numerous viruses package their dsDNA genome into preformed capsids through a portal gatekeeper that is subsequently closed. We report the structure of the DNA gatekeeper complex of bacteriophage SPP1 (gp612gp1512gp166) in the post-DNA packaging state at 2.7 Å resolution obtained by single particle cryo-electron microscopy. Comparison of the native SPP1 complex with assembly-naïve structures of individual components uncovered the complex program of conformational changes leading to its assembly. After DNA packaging, gp15 binds via its C-terminus to the gp6 oligomer positioning gp15 subunits for oligomerization. Gp15 refolds its inner loops creating an intersubunit β-barrel that establishes different types of contacts with six gp16 subunits. Gp16 binding and oligomerization is accompanied by folding of helices that close the portal channel to keep the viral genome inside the capsid. This mechanism of assembly has broad functional and evolutionary implications for viruses of the prokaryotic tailed viruses-herpesviruses lineage.
Structural basis of RNA polymerase II transcription on the chromatosome containing linker histone H1
Authors: Hirano Rina , Ehara Haruhiko , Kujirai Tomoya , Uejima Tamami , Takizawa Yoshimasa , Sekine Shun-ichi , Kurumizaka Hitoshi
Published: November 2022

In chromatin, linker histone H1 binds to nucleosomes, forming chromatosomes, and changes the transcription status. However, the mechanism by which RNA polymerase II (RNAPII) transcribes the DNA in the chromatosome has remained enigmatic. Here we report the cryo-electron microscopy (cryo-EM) structures of transcribing RNAPII-chromatosome complexes (forms I and II), in which RNAPII is paused at the entry linker DNA region of the chromatosome due to H1 binding. In the form I complex, the H1 bound to the nucleosome restricts the linker DNA orientation, and the exit linker DNA is captured by the RNAPII DNA binding cleft. In the form II complex, the RNAPII progresses a few bases ahead by releasing the exit linker DNA from the RNAPII cleft, and directly clashes with the H1 bound to the nucleosome. The transcription elongation factor Spt4/5 masks the RNAPII DNA binding region, and drastically reduces the H1-mediated RNAPII pausing.
Creb5 coordinates synovial joint formation with the genesis of articular cartilage
Authors: Zhang Cheng-Hai , Gao Yao , Hung Han-Hwa , Zhuo Zhu , Grodzinsky Alan J. , Lassar Andrew B.
Published: November 2022

While prior work has established that articular cartilage arises from Prg4-expressing perichondrial cells, it is not clear how this process is specifically restricted to the perichondrium of synovial joints. We document that the transcription factor Creb5 is necessary to initiate the expression of signaling molecules that both direct the formation of synovial joints and guide perichondrial tissue to form articular cartilage instead of bone. Creb5 promotes the generation of articular chondrocytes from perichondrial precursors in part by inducing expression of signaling molecules that block a Wnt5a autoregulatory loop in the perichondrium. Postnatal deletion of Creb5 in the articular cartilage leads to loss of both flat superficial zone articular chondrocytes coupled with a loss of both Prg4 and Wif1 expression in the articular cartilage; and a non-cell autonomous up-regulation of Ctgf. Our findings indicate that Creb5 promotes joint formation and the subsequent development of articular chondrocytes by driving the expression of signaling molecules that both specify the joint interzone and simultaneously inhibit a Wnt5a positive-feedback loop in the perichondrium.
Persistent high latitude amplification of the Pacific Ocean over the past 10 million years
Authors: Liu Xiaoqing , Huber Matthew , Foster Gavin L. , Dessler Andrew , Zhang Yi Ge
Published: November 2022

While high latitude amplification is seen in modern observations, paleoclimate records, and climate modeling, better constraints on the magnitude and pattern of amplification would provide insights into the mechanisms that drive it, which remain actively debated. Here we present multi-proxy multi-site paleotemperature records over the last 10 million years from the Western Pacific Warm Pool (WPWP) – the warmest endmember of the global ocean that is uniquely important in the global radiative feedback change. These sea surface temperature records, based on lipid biomarkers and seawater Mg/Ca-adjusted foraminiferal Mg/Ca, unequivocally show warmer WPWP in the past, and a secular cooling over the last 10 million years. Compiling these data with existing records reveals a persistent, nearly stationary, extratropical response pattern in the Pacific in which high latitude (~50°N) temperatures increase by ~2.4° for each degree of WPWP warming. This relative warming pattern is also evident in model outputs of millennium-long climate simulations with quadrupling atmospheric CO2, therefore providing a strong constraint on the future equilibrium response of the Earth System.
A diverse Ediacara assemblage survived under low-oxygen conditions
Authors: Cherry Lucas B. , Gilleaudeau Geoffrey J. , Grazhdankin Dmitriy V. , Romaniello Stephen J. , Martin Aaron J. , Kaufman Alan J.
Published: November 2022

The Ediacaran biota were soft-bodied organisms, many with enigmatic phylogenetic placement and ecology, living in marine environments between 574 and 539 million years ago. Some studies hypothesize a metazoan affinity and aerobic metabolism for these taxa, whereas others propose a fundamentally separate taxonomic grouping and a reliance on chemoautotrophy. To distinguish between these hypotheses and test the redox-sensitivity of Ediacaran organisms, here we present a high-resolution local and global redox dataset from carbonates that contain in situ Ediacaran fossils from Siberia. Cerium anomalies are consistently >1, indicating that local environments, where a diverse Ediacaran assemblage is preserved in situ as nodules and carbonaceous compressions, were pervasively anoxic. Additionally, δ238U values match other terminal Ediacaran sections, indicating widespread marine euxinia. These data suggest that some Ediacaran biotas were tolerant of at least intermittent anoxia, and thus had the capacity for a facultatively anaerobic lifestyle. Alternatively, these soft-bodied Ediacara organisms may have colonized the seafloor during brief oxygenation events not recorded by redox proxy data. Broad temporal correlations between carbon, sulfur, and uranium isotopes further highlight the dynamic redox landscape of Ediacaran-Cambrian evolutionary events.
Fast light-switchable polymeric carbon nitride membranes for tunable gas separation
Authors: Ashirov Timur , Siena Julya Stein , Zhang Mengru , Ozgur Yazaydin A. , Antonietti Markus , Coskun Ali
Published: November 2022

Switchable gas separation membranes are intriguing systems for regulating the transport properties of gases. However, existing stimuli-responsive gas separation membranes suffer from either very slow response times or require high energy input for switching to occur. Accordingly, herein, we introduced light-switchable polymeric carbon nitride (pCN) gas separation membranes with fast response times prepared from melamine precursor through in-situ formation and deposition of pCN onto a porous support using chemical vapor deposition. Our systematic analysis revealed that the gas transport behavior upon light irradiation is fully governed by the polarizability of the permeating gas and its interaction with the charged pCN surface, and can be easily tuned either by controlling the power of the light and/or the duration of irradiation. We also demonstrated that gases with higher polarizabilities such as CO2 can be separated from gases with lower polarizability like H2 and He effectively with more than 22% increase in the gas/CO2 selectivity upon light irradiation. The membranes also exhibited fast response times (<1 s) and can be turned “on” and “off” using a single light source at 550 nm.
Arginine-modified black phosphorus quantum dots with dual excited states for enhanced electrochemiluminescence in bioanalysis
Authors: Yu Siqi , Du Yu , Niu Xianghong , Li Guangming , Zhu Da , Yu Qian , Zou Guizheng , Ju Huangxian
Published: November 2022

The electrochemiluminescence (ECL) is generally emitted via radiative transition of singlet or triplet excited state (S1 or T1). Herein, an ECL mechanism with the transitions of both S1 and T1 of black phosphorus quantum dots (BPQDs) is found, and an arginine (Arg) modification strategy is proposed to passivate the surface oxidation defects of BPQDs, which could modulate the excited states for enhancing the ECL efficiency of BPQDs. The Arg modification leads to greater spatial overlap of highest and lowest occupied molecular orbitals, and spectral shift of radiative transitions, and improves the stability of anion radical of BPQDs. To verify the application of the proposed mechanism, it is used to construct a sensitive method for conveniently evaluating the inhibiting efficiency of cyclo-arginine-glycine-aspartic acid-d-tyrosine-lysine to cell surface integrin by using Arg containing peptide modified BPQDs as signal tag. The dual excited states mediated ECL emitters provide a paradigm for adjustable ECL generation and extend the application of ECL analysis.
Chiral nanocrystals grown from MoS2 nanosheets enable photothermally modulated enantioselective release of antimicrobial drugs
Authors: Li Bang Lin , Luo Jun Jiang , Zou Hao Lin , Zhang Qing-Meng , Zhao Liu-Bin , Qian Hang , Luo Hong Qun , Leong David Tai , Li Nian Bing
Published: November 2022

The transfer of the concept of chirality from molecules to synthesized nanomaterials has attracted attention amongst multidisciplinary teams. Here we demonstrate heterogeneous nucleation and anisotropic accumulation of Au nanoparticles on multilayer MoS2 planes to form chiroptically functional nanomaterials. Thiol amino acids with chiral conformations modulate asymmetric growth of gold nanoarchitectures on seeds of highly faceted Au/MoS2 heterostructures. Consequently, dendritic plasmonic nanocrystals with partial chiral morphologies are synthesized. The chirality of dendritic nanocrystals inherited from cysteine molecules refers to the structural characteristics and includes specific recognition of enantiomeric molecules. With integration of the intrinsic photothermal properties and inherited enantioselective characteristics, dendritic Au/MoS2 heterostructures exhibit chirality-dependent release of antimicrobial drugs from hydrogel substrates when activated by exogenous infrared irradiation. A three-in-one strategy involving synthesis of chiral dendritic heterostructures, enantioselective recognition, and controlled drug release system is presented, which improves nanomaterial synthetic technology and enhances our understanding of crucial chirality information.
Orthogonal glycolytic pathway enables directed evolution of noncanonical cofactor oxidase
Authors: King Edward , Maxel Sarah , Zhang Yulai , Kenney Karissa C. , Cui Youtian , Luu Emma , Siegel Justin B. , Weiss Gregory A. , Luo Ray , Li Han
Published: November 2022

Noncanonical cofactor biomimetics (NCBs) such as nicotinamide mononucleotide (NMN+) provide enhanced scalability for biomanufacturing. However, engineering enzymes to accept NCBs is difficult. Here, we establish a growth selection platform to evolve enzymes to utilize NMN+-based reducing power. This is based on an orthogonal, NMN+-dependent glycolytic pathway in Escherichia coli which can be coupled to any reciprocal enzyme to recycle the ensuing reduced NMN+. With a throughput of >106 variants per iteration, the growth selection discovers a Lactobacillus pentosus NADH oxidase variant with ~10-fold increase in NMNH catalytic efficiency and enhanced activity for other NCBs. Molecular modeling and experimental validation suggest that instead of directly contacting NCBs, the mutations optimize the enzyme’s global conformational dynamics to resemble the WT with the native cofactor bound. Restoring the enzyme’s access to catalytically competent conformation states via deep navigation of protein sequence space with high-throughput evolution provides a universal route to engineer NCB-dependent enzymes.
Dynamic complex opto-magnetic holography
Authors: Makowski M. , Bomba J. , Frej A. , Kolodziejczyk M. , Sypek M. , Shimobaba T. , Ito T. , Kirilyuk A. , Stupakiewicz A.
Published: November 2022

Despite recent significant progress in real-time, large-area computer-generated holography, its memory requirements and computational loads will be hard to tackle for several decades to come with the current paradigm based on a priori calculations and bit-plane writing to a spatial light modulator. Here we experimentally demonstrate a holistic approach to serial computation and repeatable writing of computer-generated dynamic holograms without Fourier transform, using minimal amounts of computer memory. We use the ultrafast opto-magnetic recording of holographic patterns in a ferrimagnetic film with femtosecond laser pulses, driven by the on-the-fly hardware computation of a single holographic point. The intensity-threshold nature of the magnetic medium allows sub-diffraction-limited, point-by-point toggling of arbitrarily localized magnetic spots on the sample, according to the proposed circular detour-phase encoding, providing complex modulation and symmetrical suppression of upper diffractive orders and conjugated terms in holographically reconstructed 3-D images.
Energy cascades in donor-acceptor exciton-polaritons observed by ultrafast two-dimensional white-light spectroscopy
Authors: Son Minjung , Armstrong Zachary T. , Allen Ryan T. , Dhavamani Abitha , Arnold Michael S. , Zanni Martin T.
Published: November 2022

Exciton-polaritons are hybrid states formed when molecular excitons are strongly coupled to photons trapped in an optical cavity. These systems exhibit many interesting, but not fully understood, phenomena. Here, we utilize ultrafast two-dimensional white-light spectroscopy to study donor-acceptor microcavities made from two different layers of semiconducting carbon nanotubes. We observe the delayed growth of a cross peak between the upper- and lower-polariton bands that is oftentimes obscured by Rabi contraction. We simulate the spectra and use Redfield theory to learn that energy cascades down a manifold of new electronic states created by intermolecular coupling and the two distinct bandgaps of the donor and acceptor. Energy most effectively enters the manifold when light-matter coupling is commensurate with the energy distribution of the manifold, contributing to long-range energy transfer. Our results broaden the understanding of energy transfer dynamics in exciton-polariton systems and provide evidence that long-range energy transfer benefits from moderately-coupled cavities.
Rad52’s DNA annealing activity drives template switching associated with restarted DNA replication
Authors: Kishkevich Anastasiya , Tamang Sanjeeta , Nguyen Michael O. , Oehler Judith , Bulmaga Elena , Andreadis Christos , Morrow Carl A. , Jalan Manisha , Osman Fekret , Whitby Matthew C.
Published: November 2022

It is thought that many of the simple and complex genomic rearrangements associated with congenital diseases and cancers stem from mistakes made during the restart of collapsed replication forks by recombination enzymes. It is hypothesised that this recombination-mediated restart process transitions from a relatively accurate initiation phase to a less accurate elongation phase characterised by extensive template switching between homologous, homeologous and microhomologous DNA sequences. Using an experimental system in fission yeast, where fork collapse is triggered by a site-specific replication barrier, we show that ectopic recombination, associated with the initiation of recombination-dependent replication (RDR), is driven mainly by the Rad51 recombinase, whereas template switching, during the elongation phase of RDR, relies more on DNA annealing by Rad52. This finding provides both evidence and a mechanistic basis for the transition hypothesis.
Chiral aldehyde-nickel dual catalysis enables asymmetric α−propargylation of amino acids and stereodivergent synthesis of NP25302
Authors: Zhu Fang , Li Chao-Xing , Wu Zhu-Lian , Cai Tian , Wen Wei , Guo Qi-Xiang
Published: November 2022

The combined catalytic systems derived from organocatalysts and transition metals exhibit powerful activation and stereoselective-control abilities in asymmetric catalysis. This work describes a highly efficient chiral aldehyde-nickel dual catalytic system and its application for the direct asymmetric α−propargylation reaction of amino acid esters with propargylic alcohol derivatives. Various structural diversity α,α−disubstituted non-proteinogenic α−amino acid esters are produced in good-to-excellent yields and enantioselectivities. Furthermore, a stereodivergent synthesis of natural product NP25302 is achieved, and a reasonable reaction mechanism is proposed to illustrate the observed stereoselectivity based on the results of control experiments, nonlinear effect investigation, and HRMS detection.
Molecular basis for glycan recognition and reaction priming of eukaryotic oligosaccharyltransferase
Authors: Ramírez Ana S. , de Capitani Mario , Pesciullesi Giorgio , Kowal Julia , Bloch Joël S. , Irobalieva Rossitza N. , Reymond Jean-Louis , Aebi Markus , Locher Kaspar P.
Published: November 2022

Oligosaccharyltransferase (OST) is the central enzyme of N-linked protein glycosylation. It catalyzes the transfer of a pre-assembled glycan, GlcNAc2Man9Glc3, from a dolichyl-pyrophosphate donor to acceptor sites in secretory proteins in the lumen of the endoplasmic reticulum. Precise recognition of the fully assembled glycan by OST is essential for the subsequent quality control steps of glycoprotein biosynthesis. However, the molecular basis of the OST-donor glycan interaction is unknown. Here we present cryo-EM structures of S. cerevisiae OST in distinct functional states. Our findings reveal that the terminal glucoses (Glc3) of a chemo-enzymatically generated donor glycan analog bind to a pocket formed by the non-catalytic subunits WBP1 and OST2. We further find that binding either donor or acceptor substrate leads to distinct primed states of OST, where subsequent binding of the other substrate triggers conformational changes required for catalysis. This alternate priming allows OST to efficiently process closely spaced N-glycosylation sites.
Increased fire activity under high atmospheric oxygen concentrations is compatible with the presence of forests
Authors: Vitali Rayanne , Belcher Claire M. , Kaplan Jed O. , Watson Andrew J.
Published: November 2022

Throughout Earth’s history, the abundance of oxygen in our atmosphere has varied, but by how much remains debated. Previously, an upper limit for atmospheric oxygen has been bounded by assumptions made regarding the fire window: atmospheric oxygen concentrations higher than 30–40% would threaten the regeneration of forests in the present world. Here we have tested these assumptions by adapting a Dynamic Global Vegetation Model to run over high atmospheric oxygen concentrations. Our results show that whilst global tree cover is significantly reduced under high O2 concentrations, forests persist in the wettest parts of the low and high latitudes and fire is more dependent on fuel moisture than O2 levels. This implies that the effect of fire on suppressing global vegetation under high O2 may be lower than previously assumed and questions our understanding of the mechanisms involved in regulating the abundance of oxygen in our atmosphere, with moisture as a potentially important factor.
Aerobic oxidation of methane significantly reduces global diffusive methane emissions from shallow marine waters
Authors: Mao Shi-Hai , Zhang Hong-Hai , Zhuang Guang-Chao , Li Xiao-Jun , Liu Qiao , Zhou Zhen , Wang Wei-Lei , Li Chun-Yang , Lu Ke-Yu , Liu Xi-Ting , Montgomery Andrew , Joye Samantha B. , Zhang Yu-Zhong , Yang Gui-Peng
Published: November 2022

Methane is supersaturated in surface seawater and shallow coastal waters dominate global ocean methane emissions to the atmosphere. Aerobic methane oxidation (MOx) can reduce atmospheric evasion, but the magnitude and control of MOx remain poorly understood. Here we investigate methane sources and fates in the East China Sea and map global MOx rates in shallow waters by training machine-learning models. We show methane is produced during methylphosphonate decomposition under phosphate-limiting conditions and sedimentary release is also source of methane. High MOx rates observed in these productive coastal waters are correlated with methanotrophic activity and biomass. By merging the measured MOx rates with methane concentrations and other variables from a global database, we predict MOx rates and estimate that half of methane, amounting to 1.8 ± 2.7 Tg, is consumed annually in near-shore waters (<50 m), suggesting that aerobic methanotrophy is an important sink that significantly constrains global methane emissions.
Plant genetic diversity affects multiple trophic levels and trophic interactions
Authors: Wan Nian-Feng , Fu Liwan , Dainese Matteo , Hu Yue-Qing , Pødenphant Kiær Lars , Isbell Forest , Scherber Christoph
Published: November 2022

Intraspecific genetic diversity is an important component of biodiversity. A substantial body of evidence has demonstrated positive effects of plant genetic diversity on plant performance. However, it has remained unclear whether plant genetic diversity generally increases plant performance by reducing the pressure of plant antagonists across trophic levels for different plant life forms, ecosystems and climatic zones. Here, we analyse 4702 effect sizes reported in 413 studies that consider effects of plant genetic diversity on trophic groups and their interactions. We found that that increasing plant genetic diversity decreased the performance of plant antagonists including invertebrate herbivores, weeds, plant-feeding nematodes and plant diseases, while increasing the performance of plants and natural enemies of herbivores. Structural equation modelling indicated that plant genetic diversity increased plant performance partly by reducing plant antagonist pressure. These results reveal that plant genetic diversity often influences multiple trophic levels in ways that enhance natural pest control in managed ecosystems and consumer control of plants in natural ecosystems for sustainable plant production.
Transfer efficiency of organic carbon in marine sediments
Authors: Bradley James A. , Hülse Dominik , LaRowe Douglas E. , Arndt Sandra
Published: November 2022

Quantifying the organic carbon (OC) sink in marine sediments is crucial for assessing how the marine carbon cycle regulates Earth’s climate. However, burial efficiency (BE) – the commonly-used metric reporting the percentage of OC deposited on the seafloor that becomes buried (beyond an arbitrary and often unspecified reference depth) – is loosely defined, misleading, and inconsistent. Here, we use a global diagenetic model to highlight orders-of-magnitude differences in sediment ages at fixed sub-seafloor depths (and vice-versa), and vastly different BE’s depending on sediment depth or age horizons used to calculate BE. We propose using transfer efficiencies (Teff’s) for quantifying sediment OC burial: Teff is numerically equivalent to BE but requires precise specification of spatial or temporal references, and emphasizes that OC degradation continues beyond these horizons. Ultimately, quantifying OC burial with precise sediment-depth and sediment-age-resolved metrics will enable a more consistent and transferable assessment of OC fluxes through the Earth system.
A new two-decade (2001–2019) high-resolution agricultural primary productivity dataset for India
Authors: Gangopadhyay Prasun K. , Shirsath Paresh B. , Dadhwal Vinay K. , Aggarwal Pramod K.
Published: November 2022

The present study describes a new dataset that estimates seasonally integrated agricultural gross primary productivity (GPP). Several models are being used to estimate GPP using remote sensing (RS) for regional and global studies. Using biophysical and climatic variables (MODIS, SBSS, ECWMF reanalysis etc.) and validated by crop statistics, the present study provides a new dataset of agricultural GPP for monsoon and winter seasons in India for two decades (2001–2019). This dataset (GPPCY-IN) is based on the light use efficiency (LUE) principle and applied a dynamic LUE for each year and season to capture the seasonal variations more efficiently. An additional dataset (NGPPCY-IN) is also derived from crop production statistics and RS GPP to translate district-level statistics at the pixel level. Along with validation with crop statistics, the derived dataset was also compared with in situ GPP estimations. This dataset will be useful for many applications and has been created for estimating integrated yield loss by taking GPP as a proxy compared to resource and time-consuming field-based methods for crop insurance.
SURE 2.0 – New release of the worldwide database of surface ruptures for fault displacement hazard analyses
Authors: Nurminen Fiia , Baize Stéphane , Boncio Paolo , Blumetti Anna Maria , Cinti Francesca R. , Civico Riccardo , Guerrieri Luca
Published: November 2022

Surface rupturing data from the historical earthquakes is used for obtaining empirical regression parameters for fault displacement hazard assessment. This paper represents an additional compilation and analysis effort, extending the first version of the SUrface Ruptures due to Earthquake (SURE) database. This new release contains slip measurements and mapped surface rupture traces of 50 surface rupturing earthquakes of reverse, normal, and strike-slip kinematics occurred all over the world between 1872 and 2019. As a novelty, a ranking scheme of the rupture features is applied to all the traces and slip measurements in the database. Fault ranking introduces geology as a primary analysis tool and allows the end user to obtain regression parameters suitable for the specific geological conditions at the site of interest. SURE 2.0 dataset consists of a table containing the background information about each earthquake, a table containing the slip measurement data of each event, and a joint shapefile containing all the surface rupture traces of the events in the database.
Thirty years of volcano geodesy from space at Campi Flegrei caldera (Italy)
Authors: Polcari Marco , Borgstrom Sven , Del Gaudio Carlo , De Martino Prospero , Ricco Ciro , Siniscalchi Valeria , Trasatti Elisa
Published: November 2022

This work provides the mean ground deformation rates and ground displacement time series of the Campi Flegrei caldera (Italy) retrieved by satellite remote sensing data analysis from 1992 to 2021. Synthetic Aperture Radar (SAR) images acquired by ERS 1–2 (1992–2002), Envisat (2003–2011) and Cosmo-SkyMed (2011–2021) are processed by multi-temporal SAR Interferometry (InSAR) approach using the same technique, parameters and reference system, to obtain for the first time a homogeneous and time-continuous dataset. The validation of the InSAR products is carried out by comparison with the measurements provided by precise levelling lines and cGNSS stations. The produced outcomes offer an overview on the temporal behaviour of ground deformation at Campi Flegrei along an unprecedented time window of about 30 years and can be exploited by the scientific community for supporting and improving the knowledge of the dynamics of the caldera.
Observing flow of He II with unsupervised machine learning
Authors: Wen X. , McDonald L. , Pierce J. , Guo W. , Fitzsimmons M. R.
Published: November 2022

Time dependent observations of point-to-point correlations of the velocity vector field (structure functions) are necessary to model and understand fluid flow around complex objects. Using thermal gradients, we observed fluid flow by recording fluorescence of$${\text{He}}_{2}^{*}$$He2∗excimers produced by neutron capture throughout a ~ cm3volume. Because the photon emitted by an excited excimer is unlikely to be recorded by the camera, the techniques of particle tracking (PTV) and particle imaging (PIV) velocimetry cannot be applied to extract information from the fluorescence of individual excimers. Therefore, we applied an unsupervised machine learning algorithm to identify light from ensembles of excimers (clusters) and then tracked the centroids of the clusters using a particle displacement determination algorithm developed for PTV.
Cow dung extract mediated green synthesis of zinc oxide nanoparticles for agricultural applications
Authors: Javed Zoya , Tripathi Gyan Datta , Mishra Mansi , Gattupalli Meghana , Dashora Kavya
Published: November 2022

In the present study, zinc oxide nanoparticles (ZnO) were synthesized using cow dung extract to apply sustainable agriculture from rural resources. Studies on their antibacterial potential against E. coli DH 5 alpha indicated lower antimicrobial activities than the bulk Zn and commercial Zn nanoparticles. Compared with control and commercial ZnO nanoparticles, the maximum seed germination, root length, and shoot length were observed after the priming of synthesized ZnO NPs. This study suggests that ZnO may significantly increase seed germination and have lower antimicrobial potential. Further, the lower in-vitro cellular leakage and reactive oxygen species (ROS) production provided new hope for using cow dung extract mediated nanoparticles for agricultural and industrial applications.
Development of a new screening method for faster kinship analyses in mass disasters: a proof of concept study
Authors: Kakkar Sonia , Sarma Phulen , Panigrahi Inusha , Mandal S. P. , Shrivastava Pankaj , Kumawat R. K.
Published: November 2022

Kinship analysis in forensics is based on the calculation of the respective kinship indices. However, this calculation is only possible when the subject under identification has been associated with a particular population, whose allele frequency data is available for the particular set of STR markers used in the forensic practices. In the case of mass disasters, where a large number of individuals are to be identified, gathering the population frequency data and calculating the kinship indices can be an intricate process which requires a lot of time and huge resources. The new method of allele matching cut off score (AMCOS) developed in this study is based on the allele sharing approach. This approach simply refers to the number of shared alleles (1 or 2) between the two individuals; also known as identical by state (IBS) alleles which might have been inherited from a recent common ancestor in which the alleles are identical by descendent (IBD). In case of mass disasters, this method can be used to narrow down the number of pairs (dead and alive) to be matched for kinship without using the allele frequency data. The results obtained from this method could further be confirmed by LR based method, which uses the allele frequency data of the respective population of the pairs being tested for kinship. AMCOS method has been tested for its sensitivity, specificity and various other statistical parameters and has shown promising values for the same in various types of kinship analyses. This ascertains the authenticity and potential use of this method in forensic practice but only after its validation in a larger sample size. AMCOS method has been tested on siblings and grandparent-grandchildren by using autosomal and X-STR markers both, as the reference samples from the parents cannot always be available for the identification. The present study also compared the results shown by the autosomal and X-STR markers in siblings and grandparent-grandchildren identification, thereby suggesting the use of better set of markers on the basis of obtained values of various statistical parameters.
Phycotoxicity and catalytic reduction activity of green synthesized Oscillatoria gelatin-capped silver nanoparticles
Authors: Abo-Elmagd Rasha A. , Hamouda Ragaa A. , Hussein Mervat H.
Published: November 2022

Over the last decade, an extensive range of consumer products containing manufactured silver nanoparticles (AgNPs) have been progressively used. The unfitting usage and discharge of these materials can enable passage of AgNPs into the aquatic ecosystem causing prospective toxicological consequence. The present study shed new lights on the phycotoxicity of small (8.47–17.66 nm) and stable Oscillatoria reduced gelatin-capped silver nanoparticles (OG-AgNPs) fabricated using a completely green synthetic technique. In this work, estimating of the possible toxic effects of OG-AgNPs on two freshwater microalgae Chlorella vulgaris and Chlorella minutissima was carried. This study found that, the growth of cells and photosynthetic pigment inhibitory effects of OG-AgNPs exhibit a significant increase with increasing time and concentration compared to control. Based on the IC50 value C. vulgaris (3.705 μg/mL) was found to be more sensitive to OG-AgNPs than C. minutissima (5.8 μg/mL). This study revealed that OG-AgNPs exhibit potent phycotoxic effect against Chlorella species. Finally, the negative effect of OG-AgNPs on aquatic algae and these modifications might have severe effects on structure and function of aquatic ecosystems. Besides, the biosynthesized OG-AgNPs showed a catalytic activity in the reduction of hydrogen peroxide, one of the reactive oxygen species that represent a major threat to biological systems. This method pretends an auspicious non-skill dependent technique with a good sensitivity for determination of H2O2 concentration, particularly at trace ppm level for applying in numerous domains such as medical and industrial processes.
Additive effects of EEG neurofeedback on medications for ADHD: a systematic review and meta-analysis
Authors: Lin Feng-Li , Sun Cheuk-Kwan , Cheng Yu-Shian , Wang Ming Yu , Chung Weilun , Tzang Ruu‐Fen , Chiu Hsien‐Jane , Cheng Ying-Chih , Tu Kun-Yu
Published: November 2022

To elucidate possible additive effects of electroencephalogram-based neurofeedback (EEG-NF) on medications against the core symptoms of attention-deficit/hyperactivity disorder (ADHD), randomized controlled trials (RCTs) were retrieved from electronic databases including PubMed, EMBASE, ClinicalKey, Cochrane CENTRAL, ScienceDirect, and ClinicalTrials.gov from inception to March 2022. The primary outcomes were changes in ADHD symptoms (i.e., global, inattention, hyperactivity/impulsivity) assessed with validated rating scales, while secondary outcome was all-cause discontinuation rate. Meta-analysis of five RCTs involving 305 participants [Median age = 9.285 years (range 8.6–11.05)] with a median follow-up of 12 weeks showed additive effects of EEG-NF on medications from parents’ observations against ADHD global symptoms (Hedges’ g = 0.2898, 95%CI [0.0238; 0.5557]) and inattention symptoms (Hedges’ g = 0.3274, 95%CI [0.0493; 0.6055]). However, additive effects failed to sustain six months after EEG-NF intervention. Besides, there was no difference in improvement of hyperactivity/impulsivity from parents’ observation, attentional performance, and all-cause discontinuation rate between the two groups. Our results supported additional benefits of combining EEG-NF with medications compared to medication alone in treating global symptoms and symptoms of inattention in ADHD patients. Nevertheless, given a lack of evidence showing a correlation between underlying physiological changes and small effect sizes in our preliminary results, further studies are warranted to support our findings.
Association of dietary and lifestyle inflammation scores with muscle strength and muscle endurance among Tehranian adults
Authors: Asgari Elaheh , Djafarian Kurosh , Shab-Bidar Sakineh
Published: November 2022

Diet and lifestyle as modifiable factors play an effective role in muscle strength and muscle endurance. In addition, inflammatory reactions may have an association with the etiology of a a lower muscle strength and muscle endurance. We aimed to investigate the association of dietary and lifestyle inflammation scores (DLIS) with muscle strength and muscle endurance in a sample of Iranian adults. In this cross-sectional study, 270 adults aged 20 to 59 years (55.9% female) were selected. The dietary intakes were collected using a 168-item semi-quantitative food frequency questionnaire. The DLIS was calculated using the dietary inflammatory score (DIS), and lifestyle inflammatory score (LIS). Muscle endurance and muscle strength were measured by a digital-handgrip-dynamometer. Multivariate adjusted means for muscle strength and endurance across quartiles of the DIS, LIS, and DLIS were determined by the ANCOVA test. Multiple linear regression analysis was used to evaluate the association between inflammation scores (i.e., DIS, LIS, and DLIS), and muscle strength, muscle endurance. The DLIS ranged between −2.94 and 3.09. The adjusted P-value of muscle strength of the right hand (MSR) along quartiles of DIS was significantly lower (P = 0.024). MSR (β: −1.19; P-value: 0.020) and mean muscle strength (MMS) (β: −0.95; P-value: 0.047) had significant association with DIS. MSR (β: −0.85; P-value: 0.050) had a marginally significant association with DLIS. Overall, we found that a high adherence to a pro-inflammatory diet might be associated to a lower muscle strength. However, a lifestyle with greater inflammatory potential was not related to any components of muscle endurance. Further studies with prospective designs are needed to confirm the present findings in further details.
Fusarium chlamydosporum, causing wilt disease of chili (Capsicum annum L.) and brinjal (Solanum melongena L.) in Northern Himalayas: a first report
Authors: Parihar Tasmeen J. , Sofi Mohd. Yaseen , Rasool Rovidha S. , Khursheed Sehla , Bhat Zahoor A. , Hussain Khursheed , Dhekale Bhagyashree , Zargar Sajad Majeed , Hakak Asma S. , Shah Mehraj D. , Nehvi F. A. , Bhat M. Ashraf , Khan M. N. , Masoodi Khalid Z.
Published: November 2022

Chili (Capsicum annuum L.) and brinjal (Solanum melongena L.) are the most widely grown solanaceous crops in the world. However, their production has reduced over several years due to the attack of various fungal and bacterial pathogens and various abiotic factors. Still, the major constrain in their production are pathogens with fungal etiology, especially the fungal wilt of solanaceous crops. Fusarium oxysporum and Fusarium solani have been previously identified as the pathogens causing wilt disease in chili and brinjal. Recently, a new fungal pathogen F. equiseti has been reported as the causal agent of wilt disease infecting chili. The current study focused on identifying fungal pathogens associated with the wilted plants of chili and brinjal, collected from different parts of the Himalayan region of Kashmir valley, through morpho-cultural and molecular characterization. DNA extraction, PCR amplification, and sequencing were performed on various isolates. DNA barcoding using the internal transcribed spacer region (ITS) was used to identify the pathogen followed by the pathogenicity test. Further confirmation of the pathogen was done by sequencing of transcription elongation factor (TEF) and Calmodulin (CAL2). In current study Fusarium chlamydosporum has been reported as the wilt causing pathogen of chili and brinjal for the first time in Kashmir Himalayas.
A novel prognostic model for cutaneous melanoma based on an immune-related gene signature and clinical variables
Authors: Tang Yifan , Feng Huicong , Zhang Lupeng , Qu Chiwen , Li Jinlong , Deng Xiangyu , Zhong Suye , Yang Jun , Deng Xiyun , Zeng Xiaomin , Wang Yiren , Peng Xiaoning
Published: November 2022

Abundant evidence has indicated that the prognosis of cutaneous melanoma (CM) patients is highly complicated by the tumour immune microenvironment. We retrieved the clinical data and gene expression data of CM patients in The Cancer Genome Atlas (TCGA) database for modelling and validation analysis. Based on single-sample gene set enrichment analysis (ssGSEA) and consensus clustering analysis, CM patients were classified into three immune level groups, and the differences in the tumour immune microenvironment and clinical characteristics were evaluated. Seven immune-related CM prognostic molecules, including three mRNAs (SUCO, BTN3A1 and TBC1D2), three lncRNAs (HLA-DQB1-AS1, C9orf139 and C22orf34) and one miRNA (hsa-miR-17-5p), were screened by differential expression analysis, ceRNA network analysis, LASSO Cox regression analysis and univariate Cox regression analysis. Their biological functions were mainly concentrated in the phospholipid metabolic process, transcription regulator complex, protein serine/threonine kinase activity and MAPK signalling pathway. We established a novel prognostic model for CM integrating clinical variables and immune molecules that showed promising predictive performance demonstrated by receiver operating characteristic curves (AUC ≥ 0.74), providing a scientific basis for predicting the prognosis and improving the clinical outcomes of CM patients.
Epidemiology and outcomes for level 1 and 2 traumas during the first wave of COVID19 in a Canadian centre
Authors: Boutin S. , Elder J. , Sothilingam N. , Davis P. , Oyedokun T.
Published: November 2022

To determine if lockdown measures imposed during the first wave of the COVID19 pandemic affected trauma patterns, volumes, and outcomes in a western Canadian level 1 trauma center, we performed a retrospective cohort study assessing level 1 and 2 trauma patients presenting to our center during the initial COVID19 “lockdown” period (March 15–June 14, 2020) compared to a similar cohort of patients presenting during a “control” period 1 year prior (March 15–June 14, 2019). Overall, we saw a 7.8% reduction in trauma volumes during the lockdown period, and this was associated with a shorter average ED length of stay (6.2 ± 4.7 h vs. 9.7 ± 11.8 h, p = 0.003), reduced time to computed tomography (88.5 ± 68.2 min vs. 105.1 ± 65.5 min, p < 0.001), a reduction in intensive care unit admissions (11.0 ± 4.9% vs. 20.0 ± 15.5%, p = 0.001), and higher injury severity score (6.5 ± 7.6 vs. 6.2 ± 9.5, p = 0.04). Our findings suggest that lockdown measures imposed during the first wave of the COVID19 pandemic had a significant impact on trauma patients.
The anti-obesity effect of mulberry leaf (Mori Folium) extracts was increased by bioconversion with Pectinex
Authors: Han Joo-Hui , Lee Hyung-Won , Jung Sang-Hyuk , Cho Chong Woon , Kim Tae Jeong , Kang Jong Seong , Myung Chang-Seon
Published: November 2022

Mulberry leaf (Mori Folium) extract (MLE) is known to have anti-obesity effects. In this study, the enhanced effects of MLE after bioconversion treatment using Pectinex (BMLE) on obesity were explored, and the underlying mechanisms were investigated using the active components, neochlorogenic acid (5-CQA) and cryptochlorogenic acid (4-CQA), whose amounts were increased by bioconversion of MLE. Both MLE and BMLE inhibited lipid accumulation in 3T3-L1 adipocytes without cytotoxicity and suppressed the expression of CCAAT/enhancer-binding protein alpha (C/EBPα). In addition, MLE and BMLE decreased high-fat diet-induced adipose tissue mass expansion. Notably, BMLE significantly increased antiadipogenic and anti-obesity effects compared to MLE in vitro and in vivo. The active ingredients increased by bioconversion, 5-CQA and 4-CQA, inhibited the protein levels of C/EBPα and the mRNA levels of stearoyl-CoA desaturase 1 (Scd1). These findings provide new insights into the therapeutic possibility of using bioconversion of MLE, by which upregulation of 5-CQA and 4-CQA potently inhibits adipogenesis.
Fexinidazole interferes with the growth and structural organization of Trypanosoma cruzi
Authors: Zuma Aline Araujo , de Souza Wanderley
Published: November 2022

Fexinidazole (FEX) is a heterocyclic compound and constitutes the first 100% oral treatment drug for African trypanosomiasis. Its effectiveness against Trypanosoma brucei encouraged the investigation of its antiparasitic potential against T. cruzi, the aetiological agent of Chagas disease. Although previous studies addressed the antitrypanosomal effects of FEX, none used electron microscopy to identify the main target structures of T. brucei or T. cruzi. In this work, we used microscopy techniques to analyze the ultrastructural alterations caused by FEX in different developmental stages of T. cruzi. In addition to inhibiting T. cruzi proliferation, with IC50 of 1 µM for intracellular amastigotes, FEX promoted massive disorganization of reservosomes, the detachment of the plasma membrane, unpacking of nuclear heterochromatin, mitochondrial swelling, Golgi disruption and alterations in the kinetoplast-mitochondrion complex. Together, these observations point to FEX as a potential drug leader for further developing of chemotherapy against Chagas disease.
Self-assessment of the health status and leisure activities of individuals on haemodialysis
Authors: Cunha Alexandre Cardoso da , Santos Neto Edson Theodoro dos , Salaroli Luciane Bresciani
Published: November 2022

Self-assessment of health status is an important marker of social and health aspects. Haemodialysis is an option for renal replacement therapy that alters daily life and impacts social participation and the performance of tasks that give the subject a socially accepted role. In this scenario, leisure activities have the potential to generate well-being and are associated with several aspects of daily life, but few studies have analysed their relationship with the self-assessment of health status. This is a cross-sectional, census study with 1024 individuals from haemodialysis units of a Southeast Brazilian region, with the application of a questionnaire in 2019. We calculated the difference between the proportions of self-assessment of health status (positive and negative) and the two logistic regression models. The chances of individuals on haemodialysis negatively evaluating their health increase when they do not perform artistic leisure activities (OR 2.15; 95% CI 1.35–3.43), physical and sports activities (OR 3.20; 95% CI 1.86–5.52), intellectual (OR 2.21; 95% CI 1.44–3.41), manuals (OR 1.82; 95% CI 1.22–2.72), social (OR 2.74; 95% CI 1.74–4.31), tourist (OR 2.08; 95% CI 1.37–3.17) and idleness and contemplative (OR 1.92; 95% CI 1.29–2.85). Negative health self-assessment is associated with not practicing artistic, manual, physical and sporting, social, intellectual, tourist, and contemplative leisure activities, which have the function of providing social participation and giving meaning to life.