bluuebunny/crossref_metadata_2025 huggingface dataset:
Dental black plaque: metagenomic characterization and comparative analysis with white-plaque
Authors: Veses Verónica , González-Torres Pedro , Carbonetto Belén , del Mar Jovani-Sancho Mª , González-Martínez Raquel , Cortell-Ballester Isidoro , Sheth Chirag C.
Published: September 2020

Extrinsic black dental staining is an external dental discoloration of bacterial origin, considered a special form of dental plaque. Currently, there is no definitive therapeutic option for eliminating black stain. This study employed 16S rRNA metagenomics to analyze black stain and white-plaque samples from 27 adult volunteers. Study objectives were to: describe the microbial diversity of adult black stain samples; characterize their taxonomic profile; compare the microbiomes of black stain versus white-plaque from adult volunteers and propose a functional map of the black stain microbiome using PICRUSt2. The black stain microbiome was poorer in species diversity as compared to white-plaque. The five most abundant genera in black stain were Capnocytophaga, Leptotrichia, Fusobacterium, Corynebacterium and Streptococcus. Functional analysis of microbial species revealed conserved and consistent clustering of functional pathways within and between black stain and white-plaque microbiomes. We describe enrichment of heme biosynthetic pathways in black stain. Our results suggest that the dysbiosis in black stain resembles “orally healthy” communities. The increased abundance of heme biosynthetic pathways suggests that heme-dependent iron sequestration and subsequent metabolism are key for black stain formation. Further research should decipher the regulation of heme biosynthetic genes and characterize the temporal sequence leading to colonization and dysbiosis.
Limitations to intergenerational inheritance: subchronic paternal stress preconception does not influence offspring anxiety
Authors: Fennell K. A. , Busby R. G. G. , Li S. , Bodden C. , Stanger S. J. , Nixon B. , Short A. K. , Hannan A. J. , Pang T. Y.
Published: September 2020

Independent studies have observed that a paternal history of stress or trauma is associated with his children having a greater likelihood of developing psychopathologies such as anxiety disorders. This father-to-child effect is reproduced in several mouse models of stress, which have been crucial in developing a greater understanding of intergenerational epigenetic inheritance. We previously reported that treatment of C57Bl/6J male breeders with low-dose corticosterone (CORT) for 28 days prior to mating yielded increased anxiety-related behaviours in their male F1 offspring. The present study aimed to determine whether subchronic 7-day CORT treatment of male mice just prior to mating would be sufficient to induce intergenerational modifications of anxiety-related behaviours in offspring. We report that subchronic CORT treatment of male breeders reduced their week-on-week body weight gain and altered NR3C1 and CRH gene expression in the hypothalamus. There were no effects on sperm count and glucocorticoid receptor protein levels within the epididymal tissue of male breeders. Regarding the F1 offspring, screening for anxiety-related behaviours using the elevated-plus maze, light–dark box, and novelty-suppressed feeding test revealed no differences between the offspring of CORT-treated breeders compared to controls. Thus, it is crucial that future studies take into consideration the duration of exposure when assessing the intergenerational impacts of paternal health.
Camera-based optical palpation
Authors: Sanderson Rowan W. , Fang Qi , Curatolo Andrea , Adams Wayne , Lakhiani Devina D. , Ismail Hina M. , Foo Ken Y. , Dessauvagie Benjamin F. , Latham Bruce , Yeomans Chris , Saunders Christobel M. , Kennedy Brendan F.
Published: September 2020

Optical elastography is undergoing extensive development as an imaging tool to map mechanical contrast in tissue. Here, we present a new platform for optical elastography by generating sub-millimetre-scale mechanical contrast from a simple digital camera. This cost-effective, compact and easy-to-implement approach opens the possibility to greatly expand applications of optical elastography both within and beyond the field of medical imaging. Camera-based optical palpation (CBOP) utilises a digital camera to acquire photographs that quantify the light intensity transmitted through a silicone layer comprising a dense distribution of micro-pores (diameter, 30–100 µm). As the transmission of light through the micro-pores increases with compression, we deduce strain in the layer directly from intensity in the digital photograph. By pre-characterising the relationship between stress and strain of the layer, the measured strain map can be converted to an optical palpogram, a map of stress that visualises mechanical contrast in the sample. We demonstrate a spatial resolution as high as 290 µm in CBOP, comparable to that achieved using an optical coherence tomography-based implementation of optical palpation. In this paper, we describe the fabrication of the micro-porous layer and present experimental results from structured phantoms containing stiff inclusions as small as 0.5 × 0.5 × 1 mm. In each case, we demonstrate high contrast between the inclusion and the base material and validate both the contrast and spatial resolution achieved using finite element modelling. By performing CBOP on freshly excised human breast tissue, we demonstrate the capability to delineate tumour from surrounding benign tissue.
Vitamin D deficiency serves as a precursor to stunted growth and central adiposity in zebrafish
Authors: Knuth Megan M. , Mahapatra Debabrata , Jima Dereje , Wan Debin , Hammock Bruce D. , Law Mac , Kullman Seth W.
Published: September 2020

Emerging evidence demonstrates the importance of sufficient vitamin D (1α, 25-dihydroxyvitamin D3) levels during early life stage development with deficiencies associated with long-term effects into adulthood. While vitamin D has traditionally been associated with mineral ion homeostasis, accumulating evidence suggests non-calcemic roles for vitamin D including metabolic homeostasis. In this study, we examined the hypothesis that vitamin D deficiency (VDD) during early life stage development precedes metabolic disruption. Three dietary cohorts of zebrafish were placed on engineered diets including a standard laboratory control diet, a vitamin D null diet, and a vitamin D enriched diet. Zebrafish grown on a vitamin D null diet between 2–12 months post fertilization (mpf) exhibited diminished somatic growth and enhanced central adiposity associated with accumulation and enlargement of visceral and subcutaneous adipose depots indicative of both adipocyte hypertrophy and hyperplasia. VDD zebrafish exhibited elevated hepatic triglycerides, attenuated plasma free fatty acids and attenuated lipoprotein lipase activity consistent with hallmarks of dyslipidemia. VDD induced dysregulation of gene networks associated with growth hormone and insulin signaling, including induction of suppressor of cytokine signaling. These findings indicate that early developmental VDD impacts metabolic health by disrupting the balance between somatic growth and adipose accumulation.
Edaphic factors and plants influence denitrification in soils from a long-term arable experiment
Authors: Clark Ian M. , Fu Qingling , Abadie Maïder , Dixon Elizabeth R. , Blaud Aimeric , Hirsch Penny R.
Published: September 2020

Factors influencing production of greenhouse gases nitrous oxide (N2O) and nitrogen (N2) in arable soils include high nitrate, moisture and plants; we investigate how differences in the soil microbiome due to antecedent soil treatment additionally influence denitrification. Microbial communities, denitrification gene abundance and gas production in soils from tilled arable plots with contrasting fertilizer inputs (no N, mineral N, FYM) and regenerated woodland in the long-term Broadbalk field experiment were investigated. Soil was transferred to pots, kept bare or planted with wheat and after 6 weeks, transferred to sealed chambers with or without K15NO3 fertilizer for 4 days; N2O and N2 were measured daily. Concentrations of N2O were higher when fertilizer was added, lower in the presence of plants, whilst N2 increased over time and with plants. Prior soil treatment but not exposure to N-fertiliser or plants during the experiment influenced denitrification gene (nirK, nirS, nosZI, nosZII) relative abundance. Under our experimental conditions, denitrification generated mostly N2; N2O was around 2% of total gaseous N2 + N2O. Prior long-term soil management influenced the soil microbiome and abundance of denitrification genes. The production of N2O was driven by nitrate availability and N2 generation increased in the presence of plants.
Ghrelin reverses ductular reaction and hepatic fibrosis in a rodent model of cholestasis
Authors: Petrescu Anca D. , Grant Stephanie , Williams Elaina , Frampton Gabriel , Reinhart Evan H. , Nguyen Amy , An Suyeon , McMillin Matthew , DeMorrow Sharon
Published: September 2020

The orexigenic peptide ghrelin (Ghr) stimulates hunger signals in the hypothalamus via growth hormone secretagogue receptor (GHS-R1a). Gastric Ghr is synthetized as a preprohormone which is proteolytically cleaved, and acylated by a membrane-bound acyl transferase (MBOAT). Circulating Ghr is reduced in cholestatic injuries, however Ghr’s role in cholestasis is poorly understood. We investigated Ghr’s effects on biliary hyperplasia and hepatic fibrosis in Mdr2-knockout (Mdr2KO) mice, a recognized model of cholestasis. Serum, stomach and liver were collected from Mdr2KO and FVBN control mice treated with Ghr, des-octanoyl-ghrelin (DG) or vehicle. Mdr2KO mice had lower expression of Ghr and MBOAT in the stomach, and lower levels of circulating Ghr compared to WT-controls. Treatment of Mdr2KO mice with Ghr improved plasma transaminases, reduced biliary and fibrosis markers. In the liver, GHS-R1a mRNA was expressed predominantly in cholangiocytes. Ghr but not DG, decreased cell proliferation via AMPK activation in cholangiocytes in vitro. AMPK inhibitors prevented Ghr-induced FOXO1 nuclear translocation and negative regulation of cell proliferation. Ghr treatment reduced ductular reaction and hepatic fibrosis in Mdr2KO mice, regulating cholangiocyte proliferation via GHS-R1a, a G-protein coupled receptor which causes increased intracellular Ca2+ and activation of AMPK and FOXO1, maintaining a low rate of cholangiocyte proliferation.
Mitochondrial Calcium Uniporter (MCU) deficiency reveals an alternate path for Ca2+ uptake in photoreceptor mitochondria
Authors: Bisbach Celia M. , Hutto Rachel A. , Poria Deepak , Cleghorn Whitney M. , Abbas Fatima , Vinberg Frans , Kefalov Vladimir J. , Hurley James B. , Brockerhoff Susan E.
Published: September 2020

Rods and cones use intracellular Ca2+ to regulate many functions, including phototransduction and neurotransmission. The Mitochondrial Calcium Uniporter (MCU) complex is thought to be the primary pathway for Ca2+ entry into mitochondria in eukaryotes. We investigate the hypothesis that mitochondrial Ca2+ uptake via MCU influences phototransduction and energy metabolism in photoreceptors using a mcu-/- zebrafish and a rod photoreceptor-specific Mcu-/- mouse. Using genetically encoded Ca2+ sensors to directly examine Ca2+ uptake in zebrafish cone mitochondria, we found that loss of MCU reduces but does not eliminate mitochondrial Ca2+ uptake. Loss of MCU does not lead to photoreceptor degeneration, mildly affects mitochondrial metabolism, and does not alter physiological responses to light, even in the absence of the Na+/Ca2+, K+ exchanger. Our results reveal that MCU is dispensable for vertebrate photoreceptor function, consistent with its low expression and the presence of an alternative pathway for Ca2+ uptake into photoreceptor mitochondria.
Meter enhances the subcortical processing of speech sounds at a strong beat
Authors: Moon Il Joon , Kang Soojin , Boichenko Nelli , Hong Sung Hwa , Lee Kyung Myun
Published: September 2020

The temporal structure of sound such as in music and speech increases the efficiency of auditory processing by providing listeners with a predictable context. Musical meter is a good example of a sound structure that is temporally organized in a hierarchical manner, with recent studies showing that meter optimizes neural processing, particularly for sounds located at a higher metrical position or strong beat. Whereas enhanced cortical auditory processing at times of high metric strength has been studied, there is to date no direct evidence showing metrical modulation of subcortical processing. In this work, we examined the effect of meter on the subcortical encoding of sounds by measuring human auditory frequency-following responses to speech presented at four different metrical positions. Results show that neural encoding of the fundamental frequency of the vowel was enhanced at the strong beat, and also that the neural consistency of the vowel was the highest at the strong beat. When comparing musicians to non-musicians, musicians were found, at the strong beat, to selectively enhance the behaviorally relevant component of the speech sound, namely the formant frequency of the transient part. Our findings indicate that the meter of sound influences subcortical processing, and this metrical modulation differs depending on musical expertise.
Casein kinase 1.2 over expression restores stress resistance to Leishmania donovani HSP23 null mutants
Authors: Kröber-Boncardo Constanze , Lorenzen Stephan , Brinker Christine , Clos Joachim
Published: September 2020

Leishmania donovani is a trypanosomatidic parasite and causes the lethal kala-azar fever, a neglected tropical disease. The Trypanosomatida are devoid of transcriptional gene regulation and rely on gene copy number variations and translational control for their adaption to changing conditions. To survive at mammalian tissue temperatures, L. donovani relies on the small heat shock protein HSP23, the loss of which renders the parasites stress sensitive and impairs their proliferation. Here, we analysed a spontaneous escape mutant with wild type-like in vitro growth. Further selection of this escape strains resulted in a complete reversion of the phenotype. Whole genome sequencing revealed a correlation between stress tolerance and the massive amplification of a six-gene cluster on chromosome 35, with further analysis showing over expression of the casein kinase 1.2 gene as responsible. In vitro phosphorylation experiments established both HSP23 and the related P23 co-chaperone as substrates and modulators of casein kinase 1.2, providing evidence for another crucial link between chaperones and signal transduction protein kinases in this early branching eukaryote.
Aspirin administration might accelerate the subsidence of periprosthetic joint infection
Authors: Wei Yi Ping , Chien Ju Chun , Hsiang Wei Hsin , Yang Shan Wei , Chen Chun Yu
Published: September 2020

Since the past decade, aspirin, a popular anti-inflammatory drug, has been increasingly studied for its potential antimicrobial and antibiofilm activity with promising results, but studies were limited to in vitro and in vivo investigations. Moreover, evidence concerning the beneficial effects of aspirin on the treatment of biofilm-related infections in real-world population is limited. Thus, this study aimed to investigate whether aspirin could promote infection control for patients with periprosthetic joint infections (PJIs). A single-center database was searched. Regular aspirin exposure was defined as a prescription of aspirin for > 6 months before diagnosis of PJIs and consecutive use during the PJI treatment course at a dose ≧ 100 mg/day. General data, treatment modalities, and recurrence status were collected from medical records by an independent orthopedic surgeon. From January 01, 2010, to February 17, 2019, 88 patients who met the PJI criteria were identified and included in this study. Of these patients, 12 were taking aspirin regularly during the infectious events. In the Cox proportional hazards model, multivariate analysis revealed that the aspirin group demonstrated significant benefit via superior resolution of PJIs (HR 2.200; 95% CI 1.018–4.757; p = 0.045). In this study, aspirin is beneficial for infection resolution when combined with the current standard of PJI treatment and conventional antibiotics in the management of PJIs.
Dual COX and 5-LOX inhibition by clerodane diterpenes from seeds of Polyalthia longifolia (Sonn.) Thwaites
Authors: Nguyen Ha Thi , Vu Thien-Y. , Chandi Vishala , Polimati Haritha , Tatipamula Vinay Bharadwaj
Published: September 2020

Natural metabolites with their specific bioactivities are being considered as a potential source of materials for pharmacological studies. In this study, we successfully isolated and identified five known clerodane diterpenes, namely 16-oxo-cleroda-3,13(14)E-dien-15-oic acid (1), 16-hydroxy-cleroda-3,13-dien-15-oic acid (2), 16-hydroxy-cleroda-4(18),13-dien-16,15-olide (3), 3α,16α-dihydroxy-cleroda-4(18),13(14)Z-dien-15,16-olide (4), and 16α-hydroxy-cleroda-3,13(14)Z-dien-15,16-olide (5) from the methanolic extract of seeds of Polyalthia longifolia. Initially, all the isolated metabolites were investigated for COX-1, COX-2, and 5-LOX inhibitory activities using the standard inhibitory kits. Of which, compounds 3, 4, and 5 exhibited to be potent COX-1, COX-2, and 5-LOX inhibitors with the IC50 values similar or lower to those of the reference drugs. To understand the underlying mechanism, these compounds were subjected to molecular docking on COX-1, COX-2, and 5-LOX proteins. Interestingly, the in silico study results were in high accordance with in vitro studies where compounds 3, 4, and 5 hits assumed interactions and binding pattern comparable to that of reference drugs (indomethacin and diclofenac), as a co-crystallized ligand explaining their remarkable dual (COX/LOX) inhibitor actions. Taken together, our findings demonstrated that compounds 3, 4, and 5 functioned as dual inhibitors of COX/5-LOX and can contribute to the development of novel, more effective anti-inflammatory drugs with minimal side-effects.
Fear expressions of dogs during New Year fireworks: a video analysis
Authors: Gähwiler Sarah , Bremhorst Annika , Tóth Katinka , Riemer Stefanie
Published: September 2020

A high proportion of pet dogs show fear-related behavioural problems, with noise fears being most prevalent. Nonetheless, few studies have objectively evaluated fear expression in this species. Using owner-provided video recordings, we coded behavioural expressions of pet dogs during a real-life firework situation at New Year’s Eve and compared them to behaviour of the same dogs on a different evening without fireworks (control condition), using Wilcoxon signed ranks tests. A backwards-directed ear position, measured at the base of the ear, was most strongly associated with the fireworks condition (effect size: Cohen’s d = 0.69). Durations of locomotion (d = 0.54) and panting (d = 0.45) were also higher during fireworks than during the control condition. Vocalisations (d = 0.40), blinking (d = 0.37), and hiding (d = 0.37) were increased during fireworks, but this was not significant after sequential Bonferroni correction. This could possibly be attributed to the high inter-individual variability in the frequency of blinking and the majority of subjects not vocalising or hiding at all. Thus, individual differences must be taken into account when aiming to assess an individual’s level of fear, as relevant measures may not be the same for all individuals. Firework exposure was not associated with an elevated rate of other so-called ‘stress signals’, lip licking and yawning.
Chronic stepwise cerebral hypoperfusion differentially induces synaptic proteome changes in the frontal cortex, occipital cortex, and hippocampus in rats
Authors: Tukacs Vanda , Mittli Dániel , Györffy Balázs András , Hunyady-Gulyás Éva , Hlatky Dávid , Tóth Vilmos , Ravasz Lilla , Medzihradszky F. Katalin , Nyitrai Gabriella , Czurkó András , Juhász Gábor , Kardos József , Kékesi Katalin Adrienna
Published: September 2020

During chronic cerebral hypoperfusion (CCH), the cerebral blood flow gradually decreases, leading to cognitive impairments and neurodegenerative disorders, such as vascular dementia. The reduced oxygenation, energy supply induced metabolic changes, and insufficient neuroplasticity could be reflected in the synaptic proteome. We performed stepwise bilateral common carotid occlusions on rats and studied the synaptic proteome changes of the hippocampus, occipital and frontal cortices. Samples were prepared and separated by 2-D DIGE and significantly altered protein spots were identified by HPLC–MS/MS. We revealed an outstanding amount of protein changes in the occipital cortex compared to the frontal cortex and the hippocampus with 94, 33, and 17 proteins, respectively. The high alterations in the occipital cortex are probably due to the hypoxia-induced retrograde degeneration of the primary visual cortex, which was demonstrated by electrophysiological experiments. Altered proteins have functions related to cytoskeletal organization and energy metabolism. As CCH could also be an important risk factor for Alzheimer’s disease (AD), we investigated whether our altered proteins overlap with AD protein databases. We revealed a significant amount of altered proteins associated with AD in the two neocortical areas, suggesting a prominent overlap with the AD pathomechanism.
Entangling capacities and the geometry of quantum operations
Authors: Kao Jhih-Yuan , Chou Chung-Hsien
Published: September 2020

Quantum operations are the fundamental transformations on quantum states. In this work, we study the relation between entangling capacities of operations, geometry of operations, and positive partial transpose (PPT) states, which are an important class of states in quantum information. We show a method to calculate bounds for entangling capacity, the amount of entanglement that can be produced by a quantum operation, in terms of negativity, a measure of entanglement. The bounds of entangling capacity are found to be associated with how non-PPT (PPT preserving) an operation is. A length that quantifies both entangling capacity/entanglement and PPT-ness of an operation or state can be defined, establishing a geometry characterized by PPT-ness. The distance derived from the length bounds the relative entangling capability, endowing the geometry with more physical significance. We also demonstrate the equivalence of PPT-ness and separability for unitary operations.
Enhanced LTP of population spikes in the dentate gyrus of mice haploinsufficient for neurobeachin
Authors: Muellerleile Julia , Blistein Aline , Rohlmann Astrid , Scheiwe Frederieke , Missler Markus , Schwarzacher Stephan W. , Jedlicka Peter
Published: September 2020

Deletion of the autism candidate molecule neurobeachin (Nbea), a large PH-BEACH-domain containing neuronal protein, has been shown to affect synaptic function by interfering with neurotransmitter receptor targeting and dendritic spine formation. Previous analysis of mice lacking one allele of the Nbea gene identified impaired spatial learning and memory in addition to altered autism-related behaviours. However, no functional data from living heterozygous Nbea mice (Nbea+/−) are available to corroborate the behavioural phenotype. Here, we explored the consequences of Nbea haploinsufficiency on excitation/inhibition balance and synaptic plasticity in the intact hippocampal dentate gyrus of Nbea+/− animals in vivo by electrophysiological recordings. Based on field potential recordings, we show that Nbea+/− mice display enhanced LTP of the granule cell population spike, but no differences in basal synaptic transmission, synapse numbers, short-term plasticity, or network inhibition. These data indicate that Nbea haploinsufficiency causes remarkably specific alterations to granule cell excitability in vivo, which may contribute to the behavioural abnormalities in Nbea+/− mice and to related symptoms in patients.
Aerosolization and recovery of viable murine norovirus in an experimental setup
Authors: Alsved Malin , Widell Anders , Dahlin Henrik , Karlson Sara , Medstrand Patrik , Löndahl Jakob
Published: September 2020

Noroviruses are the major cause for viral acute gastroenteritis in the world. Despite the existing infection prevention strategies in hospitals, the disease continues to spread and causes extensive and numerous outbreaks. Hence, there is a need to investigate the possibility of airborne transmission of norovirus. In this study, we developed an experimental setup for studies on the infectivity of aerosolized murine norovirus (MNV), a model for the human norovirus. Two aerosol generation principles were evaluated: bubble bursting, a common natural aerosolization mechanism, and nebulization, a common aerosolization technique in laboratory studies. The aerosolization setup was characterized by physical and viral dilution factors, generated aerosol particle size distributions, and the viral infectivity after aerosolization. We found a lower physical dilution factor when using the nebulization generator than with the bubble bursting generator. The viral dilution factor of the system was higher than the physical dilution; however, when comparing the physical and viral dilution factors, bubble bursting generation was more efficient. The infectivity per virus was similar using either generation principle, suggesting that the generation itself had a minor impact on MNV infectivity and that instead, the effect of drying in air could be a major reason for infectivity losses.
Precision multidimensional neural population code recovered from single intracellular recordings
Authors: Johnson James K. , Geng Songyuan , Hoffman Maximilian W. , Adesnik Hillel , Wessel Ralf
Published: September 2020

Neurons in sensory cortices are more naturally and deeply integrated than any current neural population recording tools (e.g. electrode arrays, fluorescence imaging). Two concepts facilitate efforts to observe population neural code with single-cell recordings. First, even the highest quality single-cell recording studies find a fraction of the stimulus information in high-dimensional population recordings. Finding any of this missing information provides proof of principle. Second, neurons and neural populations are understood as coupled nonlinear differential equations. Therefore, fitted ordinary differential equations provide a basis for single-trial single-cell stimulus decoding. We obtained intracellular recordings of fluctuating transmembrane current and potential in mouse visual cortex during stimulation with drifting gratings. We use mean deflection from baseline when comparing to prior single-cell studies because action potentials are too sparse and the deflection response to drifting grating stimuli (e.g. tuning curves) are well studied. Equation-based decoders allowed more precise single-trial stimulus discrimination than tuning-curve-base decoders. Performance varied across recorded signal types in a manner consistent with population recording studies and both classification bases evinced distinct stimulus-evoked phases of population dynamics, providing further corroboration. Naturally and deeply integrated observations of population dynamics would be invaluable. We offer proof of principle and a versatile framework.
Dual-guiding-layer resonance structure with an embedded metasurface for quasi-critical coupling without a perfect mirror
Authors: Park Gyeong Cheol , Park Kwangwook
Published: September 2020

We propose an all-dielectric quasi-one-port resonance structure that achieves near perfect absorption without the use of a back mirror. The structure mainly consists of a high-refractive-index silicon metasurface and surrounding high-refractive-index guiding layers. The dual-guiding-layer (DGL) structure has high background reflectance and is designed to have a ratio of two decay rates into the upper and lower regions within a wider range. When an absorbing material is introduced into a DGL system, it can be designed to achieve a near critical-coupling condition by reducing the constraints in the two decay rates. By using single-layer graphene as an absorbing material, the DGL resonance structure shows an absorption of ~ 97% and a phase change of ∼ 0.95π near the wavelength of 1550 nm, confirming quasi-critical coupling. The optimized DGL structure is relatively insensitive to potential fabrication imperfections, and consequently, the expected average peak wavelength and absorption are obtained as 1549.29 nm and 96.74%, respectively. Angle-dependent absorption confirms that maximum absorption occurs under normal incidence. The DGL absorber is also designed to cover the whole C-band region, in order to meet the quasi-critical-coupling condition. All mode profiles are similarly quasi-symmetric along the metasurface due to the same DGL resonance mechanism.
Changes in transcriptomic response to salinity stress induce the brackish water adaptation in a freshwater snail
Authors: Yokomizo Takumi , Takahashi Yuma
Published: September 2020

Studying the mechanisms of the establishment of a population in a novel environment allows us to examine the process of local adaptations and subsequent range expansion. In a river system, detecting genetic or phenotypic differences between a freshwater and brackish water population could contribute to our understanding of the initial process of brackish water adaptation. Here, we investigated behavioural and gene expression responses to salt water in a freshwater and brackish water population of the freshwater snail, Semisulcospira reiniana. Although the individuals in brackish water exhibited significantly higher activity in saltwater than freshwater individuals just after sampling, the activity of freshwater individuals had increased in the second observation after rearing, suggesting that their salinity tolerance was plastic rather than genetic. We found 476 and 1002 differentially expressed genes across salinity conditions in the freshwater and brackish water populations, respectively. The major biological process involved in the salinity response of the freshwater population was the biosynthesis and metabolic processing of nitrogen-containing compounds, but that of the brackish water population was influenced by the chitin metabolic process. These results suggest that phenotypic plasticity induces adaptation to brackish water in the freshwater snail by modifying its physiological response to salinity.
Evaluation of anatomical and physiological traits of Solanum pennellii Cor. associated with plant yield in tomato plants under water-limited conditions
Authors: Dariva Françoise Dalprá , Copati Mariane Gonçalves Ferreira , Pessoa Herika Paula , Alves Flávia Maria , Dias Felipe de Oliveira , Picoli Edgard Augusto de Toledo , da Cunha Fernando França , Nick Carlos
Published: September 2020

Although intensively studied, few works had looked into S. pennellii’s ability to cope with water-deficit conditions from a breeding point of view. In this study, we assessed potential traits of S. pennellii, that had previously been linked to high yields in other plant species, under long-term water-limited conditions and made a parallel with plant yield. For this purpose, the drought-resistant tomato genotypes IL 3–5 and IL 10–1, and the drought-sensitive IL 2–5 and IL 7–1 at seed level, together with both parents the S. pennellii accession LA 716 and the cultivar M82 were kept at 50 and 100% ASW throughout the growing season. Our findings confirm the superiority of LA 716 under water-limited conditions compared to the other S. lycopersicum genotypes in terms of plant water status maintenance. Percentual reduction on plant yield was higher in IL 3–5 and IL 10–1 than in M82 plants, indicating no correlation between drought resistance on germination and plant productive stages. A strong positive correlation was found between fruit yield and A, gs, and Ψleaf at 50% ASW, suggesting these traits as important selection criteria. LT and gmin, LA 716’s most promising traits, did not show a linear correlation with fruit yield under low water regimes. This study unravels traits behind tomato performance under water-limited conditions and should work as guidance for breeders aiming at developing drought-resistant tomato cultivars.
Regeneration of unconventional natural gas by methanogens co-existing with sulfate-reducing prokaryotes in deep shale wells in China
Authors: Zhang Yimeng , Yu Zhisheng , Zhang Yiming , Zhang Hongxun
Published: September 2020

Biogenic methane in shallow shale reservoirs has been proven to contribute to economic recovery of unconventional natural gas. However, whether the microbes inhabiting the deeper shale reservoirs at an average depth of 4.1 km and even co-occurring with sulfate-reducing prokaryote (SRP) have the potential to produce biomethane is still unclear. Stable isotopic technique with culture-dependent and independent approaches were employed to investigate the microbial and functional diversity related to methanogenic pathways and explore the relationship between SRP and methanogens in the shales in the Sichuan Basin, China. Although stable isotopic ratios of the gas implied a thermogenic origin for methane, the decreased trend of stable carbon and hydrogen isotope value provided clues for increasing microbial activities along with sustained gas production in these wells. These deep shale-gas wells harbored high abundance of methanogens (17.2%) with ability of utilizing various substrates for methanogenesis, which co-existed with SRP (6.7%). All genes required for performing methylotrophic, hydrogenotrophic and acetoclastic methanogenesis were present. Methane production experiments of produced water, with and without additional available substrates for methanogens, further confirmed biomethane production via all three methanogenic pathways. Statistical analysis and incubation tests revealed the partnership between SRP and methanogens under in situ sulfate concentration (~ 9 mg/L). These results suggest that biomethane could be produced with more flexible stimulation strategies for unconventional natural gas recovery even at the higher depths and at the presence of SRP.
RNA-cDNA hybrids mediate transposition via different mechanisms
Authors: Todd Lauren A. , Hall Amanda C. , Pietrobon Violena , Chan Janet N. Y. , Laflamme Guillaume , Mekhail Karim
Published: September 2020

Retrotransposons can represent half of eukaryotic genomes. Retrotransposon dysregulation destabilizes genomes and has been linked to various human diseases. Emerging regulators of retromobility include RNA–DNA hybrid-containing structures known as R-loops. Accumulation of these structures at the transposons of yeast 1 (Ty1) elements has been shown to increase Ty1 retromobility through an unknown mechanism. Here, via a targeted genetic screen, we identified the rnh1Δ rad27Δ yeast mutant, which lacked both the Ty1 inhibitor Rad27 and the RNA–DNA hybrid suppressor Rnh1. The mutant exhibited elevated levels of Ty1 cDNA-associated RNA–DNA hybrids that promoted Ty1 mobility. Moreover, in this rnh1Δ rad27Δ mutant, but not in the double RNase H mutant rnh1Δ rnh201Δ, RNA–DNA hybrids preferentially existed as duplex nucleic acid structures and increased Ty1 mobility in a Rad52-dependent manner. The data indicate that in cells lacking RNA–DNA hybrid and Ty1 repressors, elevated levels of RNA-cDNA hybrids, which are associated with duplex nucleic acid structures, boost Ty1 mobility via a Rad52-dependent mechanism. In contrast, in cells lacking RNA–DNA hybrid repressors alone, elevated levels of RNA-cDNA hybrids, which are associated with triplex nucleic acid structures, boost Ty1 mobility via a Rad52-independent process. We propose that duplex and triplex RNA–DNA hybrids promote transposon mobility via Rad52-dependent or -independent mechanisms.
Breast cancer biomarker detection through the photoluminescence of epitaxial monolayer MoS2 flakes
Authors: Catalán-Gómez Sergio , Briones María , Cortijo-Campos Sandra , García-Mendiola Tania , de Andrés Alicia , Garg Sourav , Kung Patrick , Lorenzo Encarnación , Pau Jose Luis , Redondo-Cubero Andrés
Published: September 2020

In this work we report on the characterization and biological functionalization of 2D MoS2flakes, epitaxially grown on sapphire, to develop an optical biosensor for the breast cancer biomarker miRNA21. The MoS2flakes were modified with a thiolated DNA probe complementary to the target biomarker. Based on the photoluminescence of MoS2, the hybridization events were analyzed for the target (miRNA21c) and the control non-complementary sequence (miRNA21nc). A specific redshift was observed for the hybridization with miRNA21c, but not for the control, demonstrating the biomarker recognition via PL. The homogeneity of these MoS2platforms was verified with microscopic maps. The detailed spectroscopic analysis of the spectra reveals changes in the trion to excitation ratio, being the redshift after the hybridization ascribed to both peaks. The results demonstrate the benefits of optical biosensors based on MoS2monolayer for future commercial devices.
Angular super-resolution retrieval in small-angle X-ray scattering
Authors: Gutman Benjamin , Mrejen Michael , Shabat Gil , Avinery Ram , Shkolnisky Yoel , Beck Roy
Published: September 2020

Small-angle X-ray scattering (SAXS) techniques enable convenient nanoscopic characterization for various systems and conditions. Unlike synchrotron-based setups, lab-based SAXS systems intrinsically suffer from lower X-ray flux and limited angular resolution. Here, we develop a two-step retrieval methodology to enhance the angular resolution for given experimental conditions. Using minute hardware additions, we show that translating the X-ray detector in subpixel steps and modifying the incoming beam shape results in a set of 2D scattering images, which is sufficient for super-resolution SAXS retrieval. The technique is verified experimentally to show superior resolution. Such advantages have a direct impact on the ability to resolve finer nanoscopic structures and can be implemented in most existing SAXS apparatuses both using synchrotron- and laboratory-based sources.
Eco-friendly approach for biosorption of Pb2+ and carcinogenic Congo red dye from binary solution onto sustainable Ulva lactuca biomass
Authors: El-Ahmady El-Naggar Noura , Rabei Nashwa H. , El-Malkey Sahar E.
Published: September 2020

Dyes constitute an important group of organic contaminants and are recognized for its harmful effects on the aquatic environments and humans. Heavy metals are also the largest group of inorganic pollutants due to their accumulation in the environment, contaminate food chains and cause adverse effects on the living organisms. Biosorption capacity ofUlva lactucabiomass was assessed in batch experiments for simultaneous removal of Pb2+and Congo red dye from binary solution. The process variables effects on Congo red dye and Pb2+removal percentages were explored by performing 50 experiments using Face-centered central composite design. The highest removal percentages of Congo red dye (97.89%) and Pb2+(98.78%) were achieved in the run no. 24, using 100 mg/L Congo red dye, 200 mg/L Pb2+, 3 g/L algal biomass, initial pH 6 and contact time was 120 min at 30 °C. FTIR analysis of the algal biomass showed the existence of many functional groups responsible for the biosorption process. After the biosorption process, SEM analysis revealed obvious morphological changes including surface shrinkage and the presence of new glossy Pb2+particles, and the EDS spectra reveals presence of additional Pb2+peak confirming the capacity ofUlva lactucabiomass to remove Pb2+from binary solution.
Consequences of different sample drying temperatures for accuracy of biomass inventories in forest ecosystems
Authors: Jagodziński Andrzej M. , Dyderski Marcin K. , Gęsikiewicz Kamil , Horodecki Paweł
Published: September 2020

Biomass estimation is one of the crucial tasks of forest ecology. Drying tree material is a crucial stage of preparing biomass estimation tools. However, at this step researchers use different drying temperatures, but we do not know how this influences accuracy of models. We aimed to assess differences in dry biomass between two drying temperatures (75 °C and 105 °C) in tree biomass components and to provide coefficients allowing for recalculation between the given temperatures. We used a set of 1440 samples from bark, branches, foliage and wood of eight European tree species: Abies alba Mill., Alnus glutinosa (L.) Gaertn., Betula pendula Roth., Fagus sylvatica L., Larix decidua Mill., Picea abies (L.) H. Karst., Pinus sylvestris L. and Quercus robur L. The differences between drying temperatures were 1.67%, 1.76%, 2.20% and 0.96% of sample dry masses of bark, branches, foliage and stem wood, respectively. Tree species influenced these differences. Our study provided coefficients allowing for recalculation of masses between the two temperatures, to unify results from different studies. However, the difference in dry mass between the two temperatures studied is lower than the range of uncertainty of biomass models, thus its influence on results of large-scale biomass assessments is low.
Revisiting the physical mutagenesis for sugarcane improvement: a stomatal prospective
Authors: Yasmeen Shafquat , Khan Muhammad Tahir , Khan Imtiaz Ahmed
Published: September 2020

This study was conducted to investigate the influence of gamma rays on stomatal parameters and the interaction of these traits with agronomy of the sugarcane crop. Three genotypes of sugarcane (NIA-0819, NIA-98, and BL4) were exposed to four doses of gamma radiation (10, 20, 30, and 40 Gy) and then subjected to field trials. Stomatal length, width, and density were observed using scanning electron microscopy. Moreover, agronomic and sugar-related characteristics of the crop were determined at maturity. The stomatal parameters augmented at two lower doses of gamma radiation (10 and 20 Gy) and declined under higher doses (30 and 40 Gy). The maximum stomatal length was observed in NIA-0819 at 10 Gy (63.71 µm), whereas NIA-98 and BL4 demonstrated highest stomatal length under 20 Gy (54.11 and 57.40 µm, respectively), indicating a role of genetic factors in varietal response. Similar trend was noticed for stomatal width and density as well. The lowermost treatment (10 Gy) of NIA-0819 produced maximum stomatal density (115.31 stomata mm-2 on the abaxial surface). Adaxial stomatal density was significantly lower than the abaxial one. Sugar quality attributes revealed a different tendency. Sucrose contents of BL4 increased gradually from 12.33% at control to 14.54% at 40 Gy. Yield and yield-contributing traits of genotypes indicated a strong positive correlation with the stomatal parameters. The present study suggested that gamma radiations cause variations in stomatal characteristics of sugarcane. These changes further influence the photosynthetic activity and instigate a direct impact on the agronomic performance of the crop.
Solvothermal synthesis of Fe3O4 nanospheres for high-performance electrochemical non-enzymatic glucose sensor
Authors: Xu Jiasheng , Sun Yuting , Zhang Jie
Published: September 2020

Ferroferric oxide (Fe3O4) nanospheres have been synthesized via a facile solvothermal procedure to serve as an electrode material for high performance non-enzymatic glucose sensor. The as-synthesized Fe3O4 nanospheres with a uniform size from 16 to 18 nm, which can increase the reaction contact area and the active sites in the process of glucose detection. Benefiting from the particular nanoscale structure, the Fe3O4 nanospheres obviously enhanced the activity of electrocatalytic oxidation towards glucose. When the Fe3O4 nanospheres material was used for non-enzymatic glucose sensor, several electrochemical properties including the high sensitivity 6560 μA mM−1 cm−2 (0.1–1.1 mM), limit of detection 33 μM (S/N = 3) and good long-term stability were well demonstrated. Furthermore, Fe3O4 nanospheres electrode confirmed the excellent performance of selectivity in glucose detection with the interfering substances existed such as urea, citric acid, ascorbic acid, and NaCl. Due to the excellent electrocatalytic activity in alkaline solution, the Fe3O4 nanospheres material can be considered as a promising candidate in blood glucose monitoring.
Leaf versus whole-canopy remote sensing methodologies for crop monitoring under conservation agriculture: a case of study with maize in Zimbabwe
Authors: Gracia-Romero Adrian , Kefauver Shawn C. , Vergara-Díaz Omar , Hamadziripi Esnath , Zaman-Allah Mainassara A. , Thierfelder Christian , Prassana Boddupalli M. , Cairns Jill E. , Araus José L.
Published: September 2020

Enhancing nitrogen fertilization efficiency for improving yield is a major challenge for smallholder farming systems. Rapid and cost-effective methodologies with the capability to assess the effects of fertilization are required to facilitate smallholder farm management. This study compares maize leaf and canopy-based approaches for assessing N fertilization performance under different tillage, residue coverage and top-dressing conditions in Zimbabwe. Among the measurements made on individual leaves, chlorophyll readings were the best indicators for both N content in leaves (R < 0.700) and grain yield (GY) (R < 0.800). Canopy indices reported even higher correlation coefficients when assessing GY, especially those based on the measurements of the vegetation density as the green area indices (R < 0.850). Canopy measurements from both ground and aerial platforms performed very similar, but indices assessed from the UAV performed best in capturing the most relevant information from the whole plot and correlations with GY and leaf N content were slightly higher. Leaf-based measurements demonstrated utility in monitoring N leaf content, though canopy measurements outperformed the leaf readings in assessing GY parameters, while providing the additional value derived from the affordability and easiness of using a pheno-pole system or the high-throughput capacities of the UAVs.
Retraction Note: The diagnostic nomogram of platelet-based score models for hepatic alveolar echinococcosis and atypical liver cancer
Authors: Du Qiancheng , Wang Yanyan , Guan Shihao , Hu Chenliang , Li Mengxuan , Zhou Ling , Zhang Mengzhao , Chen Yichong , Mei Xuepeng , Sun Jian , Zhou Ying
Published: September 2020

Editor's Note: this Article has been retracted; the Retraction Note is available at https://www.nature.com/articles/s41598-020-73758-x
Semi-transparent quaternary oxynitride photoanodes on GaN underlayers
Authors: Ma Zili , Piętak Karolina , Piątek Jędrzej , Reed DeMoulpied Justin , Rokicińska Anna , Kuśtrowski Piotr , Dronskowski Richard , Zlotnik Sebastian , Coridan Robert H. , Slabon Adam
Published: September 2020

Beyond semi-transparent Ta3N5 photoanodes: a generalized approach for manufacturing of semi-transparent quaternary metal oxynitride photoanodes aiming for wireless tandem photoelectrochemical water-splitting.
Organoiridium–quinone conjugates for facile hydrogen peroxide generation
Authors: Nguyen Huong T. H. , Do Loi H.
Published: September 2020

Tethered iridium–quinone catalyst in the presence of air and sodium formate generates H2O2 more rapidly than iridium and quinone mixtures at low catalyst concentration.
Convenient two step synthesis of 29Si labelled tetraalkoxysilanes
Authors: Gericke Robert , Gondek Christoph , Stapf André , Wagler Jörg , Kroke Edwin , Brendler Erica
Published: September 2020

Starting from silicon dioxide or silicon a scalable, reliable synthesis of 29Si enriched tetraethoxysilane, an essential sol–gel precursor, is presented.
A viologen-based multifunctional Eu-MOF: photo/electro-modulated chromism and luminescence
Authors: Fu Ting , Wei Yong-Li , Zhang Chong , Li Lin-Ke , Liu Xiao-Fei , Li Hai-Yang , Zang Shuang-Quan
Published: September 2020

A novel viologen-based multifunctional Eu-MOF integrating photochromism, photomodulated fluorescence, and electrochromic and electroluminochromic properties was investigated.