bluuebunny/crossref_metadata_2025 huggingface dataset:
Rationally-designed sandwiched nanostructures boosting Fe-N based catalysts toward efficient oxygen reduction electrocatalysis in acidic medium
Authors: Liu Lingyun , Lu Tingjing , Shi Xiang , Wang Zhibo , Li Chuan , Zi Zhenfa
Published: September 2022

The development of acidic-available noble-metal-free oxygen reduction reaction (ORR) catalysts with high activity and good long-term durability is of significant importance for efficient proton exchange membrane fuel cells, but is still very challenging. Herein, we develop originally a facile wet-chemical-adsorption, pyrolysis and post-etching strategy to effectively intercalate Fe clusters among two nitrogen-doped carbon (NC) layers, forming unique hollow spherical nanostructures with sandwiched NC/Fe/NC shells as an active ORR catalyst. Thanks to the sandwiched nanostructure and the active Fe-N species, this as-prepared hollow sandwiched NC/Fe/NC catalyst could present superior ORR activity in an acidic medium, with a nice onset potential of 0.92 V and decent diffusion-limited current density of ~5.1 mA/cm2. The NC/Fe/NC catalyst manifests strong methanol tolerance and outstanding durability during a long-term acidic ORR operation, being a promising alternative to Pt-based catalysts toward efficient proton exchange membrane fuel cells. Synchrotron radiation characterizations and X-ray photoemission spectroscopy reveal at the atomic-level that the abundant robust Fe–N bonds presented in the sandwiched shells of hollow NC/Fe/NC spherical catalyst contribute substantially to high electrochemical activity and superior corrosion-resistance for efficient 4e¯ ORR in acidic electrolyte.
Event-based vision in magneto-optic Kerr effect microscopy
Authors: Zhang Kai , Zhao Yuelei , Chu Zhiqin , Zhou Yan
Published: September 2022

Magneto-optic Kerr effect (MOKE) microscopy is a widely used technique for observation and characterization of microscopic magnetic structures. While being efficient and easy-to-use, current commercial MOKE microscopes are not superb in time resolution, limited by the frame rate of the camera. Here, we introduce a revolutionary sensor, namely, the event camera, as a convenient add-on to traditional MOKE microscopy and explore the potential applications of event-based vision in research areas using MOKE microscopy. We use the frame stacking method to improve visibility to human eyes in generated slow motion videos. We perform a proof-of-principle feedback control experiment using the event-based vision data and characterize the overall latency of the feedback loop as short as 25 ms with our current prototype. Finally, we discuss the limitations of current event cameras in MOKE microscopy as well.
Synthesis of metastable Ruddlesden–Popper titanates, (ATiO3)n
AO, with n ≥ 20 by molecular-beam epitaxy
Authors: Barone Matthew R. , Jeong Myoungho , Parker Nicholas , Sun Jiaxin , Tenne Dmitri A. , Lee Kiyoung , Schlom Darrell G.
Published: September 2022

We outline a method to synthesize (ATiO3)nAO Ruddlesden–Popper phases with high-n, where the A-site is a mixture of barium and strontium, by molecular-beam epitaxy. The precision and consistency of the method described is demonstrated by the growth of an unprecedented (SrTiO3)50SrO epitaxial film. We proceed to investigate barium incorporation into the Ruddlesden–Popper structure, which is limited to a few percent in bulk, and we find that the amount of barium that can be incorporated depends on both the substrate temperature and the strain state of the film. At the optimal growth temperature, we demonstrate that as much as 33% barium can homogeneously populate the A-site when films are grown on SrTiO3 (001) substrates, whereas up to 60% barium can be accommodated in films grown on TbScO3 (110) substrates, which we attribute to the difference in strain. This detailed synthetic study of high n, metastable Ruddlesden–Popper phases is pertinent to a variety of fields from quantum materials to tunable dielectrics.
Environmental Fluid Dynamics
Authors: Vallero Daniel A.
Published: September 2022

This chapter introduces the principles of fluid dynamics as they apply to environmental systems.
Biotic Physics
Authors: Vallero Daniel A.
Published: September 2022

This chapter provides an overview of biophysics as it applies to microbes, flora, and fauna in the environment. It extends some concepts introduces in earlier chapters, such as microbial metabolism and growth. It also applies previously discussed abiotic physical principles to living creatures, such as water retention and uptake applied to nutrient uptake by roots and translocation in plants. It also sets the stage for upcoming chapters that consider physics in the human body, physics in pollution control technologies, and physics in environmental cleanups.
Remediation Physics
Authors: Vallero Daniel A.
Published: September 2022

Applied environmental physics is increasingly making use of decision tools, including computational and statistical approaches to extend and enhance observational measurement data. As such, this chapter explores the scientific and mathematical foundations to apply physical principles to remediate contaminated sites. It begins with a discussion on how to measure, model and interpret contaminant levels at the site to recommend and selection among scientifically sound and feasible alternatives. This is followed by ways to prepare site investigations and risk assessments that are based on credible thermodynamic and fluid dynamic principles
The Use of Higher-Order Nonlinearities: Theory
Authors: Malomed Boris A.
Published: September 2022

This chapter presents basic theoretical results, which demonstrate the possibility of the existence of stable 2D and 3D solitons, both fundamental ones and solitons with embedded vorticity, under the action of the nonlinearity, which combines competing cubic self-attractive and quintic repulsive terms. 2D vortex solitons (alias vortex rings/annuli) have their stability regions for all integer values of the winding number (topological charge, alias vorticity) S = 1, 2, 3, …, while 3D vortex solitons, shaped as vortex tori (donuts), may be stable solely with S = 1. For systems of nonlinearly coupled NLS equations with the CQ nonlinearity, results are similar for vortex solitons with identical winding numbers in both components, while 2D ring-shaped solitons with opposite vorticities, ±S, in their components (hidden-vorticity solitons) are completely unstable against spontaneous splitting. Also included are results for the effective potential of interaction between far-separated 2D and 3D fundamental and vortex solitons and for the spontaneous symmetry breaking of two-component 2D spatiotemporal optical solitons in a planar dual-core coupler. The latter setting makes it possible to introduce the concept of spatiotemporal optical vortices, which feature the vortical phase distribution in the 2D plane composed of spatial and temporal coordinates [Dror and Malomed, Phys. D 240, 526–541 (2011)]. For the comparison with the setting based on the CQ nonlinearity, the chapter includes some results for the 2D model with saturable self-focusing, where all 2D and 3D vortex solitons are unstable against splitting.
Spatially Periodic Potentials (Lattices): Experiments
Authors: Malomed Boris A.
Published: September 2022

This chapter is a relatively short one, as there are much fewer experimental results reporting the creation of stable multidimensional solitons supported by lattice potentials than the number of various theoretical predictions that are summarized in Chap. 7. It is relevant to stress that this book aims to present an overview of experimental findings that are most relevant to the topic of multidimensional solitons, but not a detailed account of experimental results and methods in this area. The results included in the chapter are the creation of stable 2D optical solitons with embedded vorticity, S = 1, and a multi-peak local density distribution, in a photorefractive material, stabilized by a virtual square-shaped photonic lattice; creation of solitons with vorticity S = 2, stabilized by a hexagonal lattice; and the making of spatiotemporal light bullets (LBs), both fundamental ones and LBs with embedded vorticity, propagating in bulk silica samples with a built-in multi-core waveguiding structure. These LBs are 3D quasi-solitons, as they exist only in a transient state. Also mentioned are experimental results demonstrating surface solitons supported by photonic lattices with an edge, and Anderson localization of the spatiotemporal propagation in a random multi-core structure.
The effect of ammoniated maize stover inclusion in diets on growth performance, physiological characteristics and meat quality in lambs
Authors: Chelopo G. M. , Marume U.
Published: September 2022

Context The exploration of alternative feed sources for lambs to offset the expensive conventional ingredients is imperative. Aims To determine whether the inclusion of graded levels of ammoniated maize stover in lamb diets will positively influence growth performance, health and meat quality. Methods Thirty-two female meatmaster lambs aged 5–6 months (eight lambs per treatment) were fed isonitrogenous and isoenergetic diets containing 0%, 10%, 20% and 40% ammoniated maize stover (AMS) over a period of 7 weeks. Key results The lambs fed the AMS10 diet had a greater feed intake than did those fed AMS0, with lambs fed AMS20 and AMS40 not different from each other. Lambs fed on AMS10 and AMS20 grew faster than those fed on AMS40, but AMS0-fed lambs did not differ from any of the other groups. Similarly, feed conversion ratio (FCR, 5.25) was greater for lambs fed on AMS40 than for those on either AMS10 or AMS20, but those on AMS0 did not differ from the other groups. There were no significant differences in any of the mean values for haematological parameters; however, haematocrit was below the normal range for healthy lambs in all dietary treatments. Inclusion of AMS had no effect on the slaughter weight of lambs or any carcass characteristics apart from the dressing percentage. The lambs fed the AMS20 diets had a significantly higher dressing percentage than did all other groups. Ultimate pH (pHu) values were significantly higher on lambs fed on AMS40 than for all other groups. pHu values among AMS0, AMS10 and AMS20 were similar. Shear force for lambs on AMS40 diet was less than that for AMS0, but neither differed significantly from the other two groups. Conclusions Observations from the study showed that ammoniated maize stover may be included into lamb diets at least at 20% without adverse effects on growth performance, the health, and meat-quality characteristics of the lambs. Implications Ammoniated maize stover can therefore be a cheaper feed source for lambs in feedlot systems as it primarily replaces lucerne and maize grain.
Corrigendum to: Understanding Praxelis (Asteraceae, Eupatorieae): an updated taxonomy with lectotypifications and morphological and distributional clarifications
Authors: Salgado Vanina G. , Grossi Mariana A. , Ribeiro Rogério N. , Proença Carolyn E. B. , Gutiérrez Diego G.
Published: September 2022

The South American genus Praxelis Cass. (Asteraceae, Eupatorieae) includes 18 species and is the second-largest genus of subtribe Praxelinae. It is distributed from Colombia, Venezuela and the Guianas, to central Argentina, southern Brazil and north-western Uruguay. Over the past 40years, one species, P. clematidea, has invaded several countries around the world. To understand Praxelis and its species, this study provides an updated taxonomy with the re-establishment of P. urticeafolim var. nanum as a synonym of P. ostenii, 16 lectotypifications, clarification of morphology and geographical distribution, brief descriptions, and the first key to all the species in the genus.
Mapping the ethical landscape of wildland fire management: setting an agendum for research and deliberation on the applied ethics of wildland fire
Authors: Goldstein Dyllan , Kennedy Eric B.
Published: September 2022

Background Virtually every decision within wildland fire management includes substantial ethical dimensions. As pressures increase with ever-growing fires, it is becoming increasingly important to develop tools for assessing and acting on the values intrinsic to wildfire management. Aims This paper aims to foster an applied ethics of wildland fire by bringing values to the forefront of wildland fire management debates, highlighting areas where ethical issues have been previously discussed, and providing a framework to assist in future discussion. Methods Through a literature review and collaborative thematic coding of a large set of ethical dilemmas, a list of ethical lenses was developed. Key results Five ethical lenses were generated from the thematic coding process: Epistemologies and Representation, Values and Priorities, Risk and Uncertainty, Power, and Metaethics. Conclusion The five lenses provide a framework to identify prospective ethical tensions in wildland fire decision-making, both within and cutting across categories. This framework provides a way of structuring future investigations into wildfire ethics, as well as a starting point for developing techniques to integrate community and stakeholder values. Implications Developing a field of applied ethics for wildland fire will help support decision-making, create space to more inclusively reflect and deliberate on values, and ensure that fire management best serves the public interest.
Lysosomal cathepsin D mediates endogenous mucin glycodomain catabolism in mammals
Authors: Pedram Kayvon , Laqtom Nouf N. , Shon D. Judy , Di Spiezio Alessandro , Riley Nicholas M. , Saftig Paul , Abu-Remaileh Monther , Bertozzi Carolyn R.
Published: September 2022

Mucins are functionally implicated in a range of human pathologies, including cystic fibrosis, influenza, bacterial endocarditis, gut dysbiosis, and cancer. These observations have motivated the study of mucin biosynthesis as well as the development of strategies for inhibition of mucin glycosylation. Mammalian pathways for mucin catabolism, however, have remained underexplored. The canonical view, derived from analysis of
N
-glycoproteins in human lysosomal storage disorders, is that glycan degradation and proteolysis occur sequentially. Here, we challenge this view by providing genetic and biochemical evidence supporting mammalian proteolysis of heavily
O
-glycosylated mucin domains without prior deglycosylation. Using activity screening coupled with mass spectrometry, we ascribed mucin-degrading activity in murine liver to the lysosomal protease cathepsin D. Glycoproteomics of substrates digested with purified human liver lysosomal cathepsin D provided direct evidence for proteolysis within densely
O
-glycosylated domains. Finally, knockout of cathepsin D in a murine model of the human lysosomal storage disorder neuronal ceroid lipofuscinosis 10 resulted in accumulation of mucins in liver-resident macrophages. Our findings imply that mucin-degrading activity is a component of endogenous pathways for glycoprotein catabolism in mammalian tissues.
The abundance, biomass, and distribution of ants on Earth
Authors: Schultheiss Patrick , Nooten Sabine S. , Wang Runxi , Wong Mark K. L. , Brassard François , Guénard Benoit
Published: September 2022

Knowledge on the distribution and abundance of organisms is fundamental to understanding their roles within ecosystems and their ecological importance for other taxa. Such knowledge is currently lacking for insects, which have long been regarded as the “little things that run the world”. Even for ubiquitous insects, such as ants, which are of tremendous ecological significance, there is currently neither a reliable estimate of their total number on Earth nor of their abundance in particular biomes or habitats. We compile data on ground-dwelling and arboreal ants to obtain an empirical estimate of global ant abundance. Our analysis is based on 489 studies, spanning all continents, major biomes, and habitats. We conservatively estimate total abundance of ground-dwelling ants at over 3 × 10
15
and estimate the number of all ants on Earth to be almost 20 × 10
15
individuals. The latter corresponds to a biomass of ∼12 megatons of dry carbon. This exceeds the combined biomass of wild birds and mammals and is equivalent to ∼20% of human biomass. Abundances of ground-dwelling ants are strongly concentrated in tropical and subtropical regions but vary substantially across habitats. The density of leaf-litter ants is highest in forests, while the numbers of actively ground-foraging ants are highest in arid regions. This study highlights the central role ants play in terrestrial ecosystems but also major ecological and geographic gaps in our current knowledge. Our results provide a crucial baseline for exploring environmental drivers of ant-abundance patterns and for tracking the responses of insects to environmental change.
A quantile integral linear model to quantify genetic effects on phenotypic variability
Authors: Miao Jiacheng , Lin Yupei , Wu Yuchang , Zheng Boyan , Schmitz Lauren L. , Fletcher Jason M. , Lu Qiongshi
Published: September 2022

Detecting genetic variants associated with the variance of complex traits, that is, variance quantitative trait loci (vQTLs), can provide crucial insights into the interplay between genes and environments and how they jointly shape human phenotypes in the population. We propose a quantile integral linear model (QUAIL) to estimate genetic effects on trait variability. Through extensive simulations and analyses of real data, we demonstrate that QUAIL provides computationally efficient and statistically powerful vQTL mapping that is robust to non-Gaussian phenotypes and confounding effects on phenotypic variability. Applied to UK Biobank (n= 375,791), QUAIL identified 11 vQTLs for body mass index (BMI) that have not been previously reported. Top vQTL findings showed substantial enrichment for interactions with physical activities and sedentary behavior. Furthermore, variance polygenic scores (vPGSs) based on QUAIL effect estimates showed superior predictive performance on both population-level and within-individual BMI variability compared to existing approaches. Overall, QUAIL is a unified framework to quantify genetic effects on the phenotypic variability at both single-variant and vPGS levels. It addresses critical limitations in existing approaches and may have broad applications in future gene–environment interaction studies.
Enhancing terahertz photonic spin Hall effect via optical Tamm state and the sensing application
Authors: Cheng Jie , Xu Jiahao , Xiang Yinjie , Liu Shengli , Chi Fengfeng , Li Bin , Dong Peng
Published: September 2022

The photonic spin Hall effect (PSHE), characterized by two splitting beams with opposite spins, has great potential applications in nano-photonic devices, optical sensing fields, and precision metrology. We present the significant enhancement of terahertz (THz) PSHE by taking advantage of the optical Tamm state (OTS) in InSb-distributed Bragg reflector (DBR) structure. The spin shift of reflected light can be dynamically tuned by the structural parameters (e.g. the thickness) of the InSb-DBR structure as well as the temperature, and the maximum spin shift for a horizontally polarized incident beam at 1.1 THz can reach up to 11.15 mm. Moreover, we propose a THz gas sensing device based on the enhanced PSHE via the strong excitation of OTS for the InSb-DBR structure with a superior intensity sensitivity of 5.873 × 104 mm/RIU and good stability. This sensor exhibits two orders of magnitude improvement compared with the similar PSHE sensor based on InSb-supported THz long-range surface plasmon resonance. These findings may provide an alternative way for the enhanced PSHE and offer the opportunity for developing new optical sensing devices.
Novel method for numerical reconstruction of grinding surfaces with specified roughness parameter set
Authors: Tang Jinyuan , Xia Fujia , Yang Duo , Xiao Chunqing
Published: September 2022

Surface roughness parameters play a decisive role on grinding surface service performance. Among 26 surface roughness parameters, closely related to the surface performance and defined by ISO25178, in the 6 categories, numerical reconstruction of grinding surfaces can only control 7 height parameters and 2 spatial parameters with inability to achieve precise control of other parameter-defined features. Therefore, a novel numerical reconstruction method for grinding surfaces with specified rough parameter set (SRPS) was proposed to solve the problem of feature loss caused by other uncontrollable parameters. Combine three characteristic coefficients of height probability density function in Johnson transformation method with four characteristic coefficients of autocorrelation function expression to construct surface reconstruction coefficient set (SRCS) and build SRPS with number of 22 in consideration of the measurement error influence and industrial application frequency. Use BP neural network to establish quantitative mapping model between SRCS and SRPS for inversion. Through introducing genetic algorithm to invert SRPS corresponding SRCS, numerical reconstruction of grinding surfaces with SRPS will be realized. Experimental results show that compared with the measured grinding surfaces, the average error in SRPS of reconstructed surfaces is basically within 10%. The research provides a new means for the study of the surface performance, which solves the problem that the traditional rough surface modeling method based on random process theory could only associate 9 roughness parameters.
A study of laves phase in high Nb non-oriented silicon steel for electric automobiles
Authors: Lin Zibo , Wu Zhongwang , Li Yiming , Ren Huiping , Jin Zili
Published: September 2022

In the study of precipitates in high-Nb non-oriented silicon steel for the rotor of electric automobiles, it was found that mass dispersed Nb-rich precipitates were formed during the rolling process of the steel, these precipitates are presumed to be Laves phases in published literatures. In this regard, two types of Laves phases of high-Nb non-oriented silicon steel for electric automobiles and their crystallographic relationship with the Fe matrix were determined using SAED, FFT and IFFT, and calculation of steel strength enhancement by precipitation strengthening. The results showed the elliptical Laves phase is Fe16Nb6Si7 and the rectangular strip Laves phase is Nb7P4, and the orientation relationship between Fe16Nb6Si7 phase and Fe matrix is : [001]Fe16Nb6Si7∥[001]Fe, [101]Fe16Nb6Si7∥[110]Fe, [113]Fe16Nb6Si7∥[112]Fe, the orientation relationship between Nb7P4 phase and Fe matrix is : [130]Nb7P4∥[001]Fe, [102]Nb7P4∥[110]Fe, [110]Nb7P4∥[112]Fe; Both Fe16Nb6Si7 and Nb7P4 precipitates have a good coherent relationship with the Fe matrix; The calculation results show that Fe16Nb6Si7, Nb7P4 and other precipitates can improve the yield strength of non-oriented silicon steel, but at the same time, the magnetic properties of the steel are expected to be negatively impacted. The research results can provide important theoretical guidance on the influence of thermo-mechanical processing on balancing the mechanical and magnetic properties of high niobium non-oriented silicon steel for electric vehicle rotor.
Experimental investigation on jute/snake grass/kenaf fiber reinforced novel hybrid composites with annona reticulata seed filler addition
Authors: Kumar R Prem , Muthukrishnan M , Sahayaraj A Felix
Published: September 2022

Natural fiber composites are hybridized nowadays to explore the synergetic effect of more fibers used in the properties of the composites. The natural fiber hybrid composite made with filler material has excellent wear resistance characteristics. This research work examined the mechanical properties, namely tensile, flexural, interlaminar shear strength, impact strengths, and hardness of the natural fiber reinforced hybrid composite that uses jute, snake grass, and kenaf fibers as reinforcement with various fiber volumes. Further, the wear behavior of the hybrid composites was enhanced by using Annona reticulata (custard apple) seed powder as a filler material. This study revealed that the sample has an equal proportion (12.5% of each) of snake grass and kenaf fiber (without filler) has excellent mechanical strengths. The wear behavior of the sample with 5 wt% filler shows a lower wear rate than other samples.
Polymeric sidewall transfer lithography
Authors: Lo Yi-Chen , Cheng Xing
Published: September 2022

This work is to demonstrate a low cost and time-conserving technique to create nano-trenches by transferring nano-scale polymeric sidewalls into substrate. The polymeric sidewall is a vertically spreading layer deposited by spin-coating a polymer solution on a vertical template. By varying processing parameters such as the solution concentration or the spin-coating speed, the dimension of the sidewall can be changed, which, after pattern transfer, also changes the nano-trench dimension. In this work, high-resolution trenches of about 15 nm have been achieved after transferring straight line sidewalls into substrate. Other than straight line sidewall patterns, this method also fabricates ring-shaped patterns including circles, squares, and concentric squares. With various shapes of sidewall patterns, this technique has a potential to implement other practical applications such as fabricating high-resolution nanoimprint molds of 15 nm.
Diverged subpopulations in tropicalUrochloa(Brachiaria) forage species indicate a role for facultative apomixis and varying ploidy in their population structure and evolution
Authors: Higgins J , Tomaszewska P , Pellny T K , Castiblanco V , Arango J , Tohme J , Schwarzacher T , Mitchell R A , Heslop-Harrison J S , De Vega J J
Published: September 2022

Background

Urochloa (syn. Brachiaria) is a genus of tropical grasses sown as forage feedstock, particularly in marginal soils. Here we aimed to clarify the genetic diversity and population structure in Urochloa species to understand better how population evolution relates to ploidy level and occurrence of apomictic reproduction.

Methods

We explored the genetic diversity of 111 accessions from the five Urochloa species used to develop commercial cultivars. These accessions were conserved from wild materials collected at their centre of origin in Africa, and they tentatively represent the complete Urochloa gene pool used in breeding programmes. We used RNA-sequencing to generate 1.1 million single nucleotide polymorphism loci. We employed genetic admixture, principal component and phylogenetic analyses to define subpopulations.

Results

We observed three highly differentiated subpopulations in U. brizantha, which were unrelated to ploidy: one intermixed with U. decumbens, and two diverged from the former and the other species in the complex. We also observed two subpopulations in U. humidicola, unrelated to ploidy; one subpopulation had fewer accessions but included the only characterized sexual accession in the species. Our results also supported a division of U. decumbens between diploids and polyploids, and no subpopulations within U. ruziziensis and U. maxima.

Conclusions

Polyploid U. decumbens are more closely related to polyploid U. brizantha than to diploid U. decumbens, which supports the divergence of both polyploid groups from a common tetraploid ancestor and provides evidence for the hybridization barrier of ploidy. The three differentiated subpopulations of apomictic polyploid U. brizantha accessions constitute diverged ecotypes, which can probably be utilized in hybrid breeding. Subpopulations were not observed in non-apomictic U. ruziziensis. Sexual Urochloa polyploids were not found (U. brizantha, U. decumbens) or were limited to small subpopulations (U. humidicola). The subpopulation structure observed in the Urochloa sexual–apomictic multiploidy complexes supports geographical parthenogenesis, where the polyploid genotypes exploit the evolutionary advantage of apomixis, i.e. uniparental reproduction and clonality, to occupy extensive geographical areas.
Anatomical determinants of gas exchange and hydraulics vary with leaf shape in soybean
Authors: Tamang Bishal G , Zhang Yanqun , Zambrano Michelle A , Ainsworth Elizabeth A
Published: September 2022

Background and aims

Leaf shape in crops can impact light distribution and carbon capture at the whole plant and canopy level. Given similar leaf inclination, narrow leaves can allow a greater fraction of incident light to pass through to lower canopy leaves by reducing leaf area index, which can potentially increase canopy-scale photosynthesis. Soybean has natural variation in leaf shape which can be utilized to optimize canopy architecture. However, the anatomical and physiological differences underlying variation in leaf shape remain largely unexplored.

Methods

In this study, we selected 28 diverse soybean lines with leaf length to width ratios (leaf ratio) ranging between 1.1 and 3.2. We made leaf cross-sectional, gas exchange, vein density and hydraulic measurements and studied their interrelationships among these lines.

Key results

Our study shows that narrow leaves tend to be thicker, with an ~30 µm increase in leaf thickness for every unit increase in leaf ratio. Interestingly, thicker leaves had a greater proportion of spongy mesophyll while the proportions of palisade and paraveinal mesophyll decreased. In addition, narrow and thicker leaves had greater photosynthesis and stomatal conductance per unit area along with greater leaf hydraulic conductance.

Conclusions

Our results suggest that selecting for narrow leaves can improve photosynthetic performance and potentially provide a yield advantage in soybean.
metabolomicsR: a streamlined workflow to analyze metabolomic data in R
Authors: Han Xikun , Liang Liming
Published: September 2022

metabolomicsR is a streamlined, flexible and user-friendly R package to preprocess, analyze and visualize metabolomic data. metabolomicsR includes comprehensive functionalities for sample and metabolite quality control, outlier detection, missing value imputation, dimensional reduction, batch effect normalization, data integration, regression, metabolite annotation and visualization of data and results. In this application note, we demonstrate the step-by-step use of the main functions from this package.

Availability and implementation

The metabolomicsR package is available via CRAN and GitHub (https://github.com/XikunHan/metabolomicsR/). A step-by-step online tutorial is available at https://xikunhan.github.io/metabolomicsR/docs/articles/Introduction.html.

Supplementary information

Supplementary data are available at Bioinformatics Advances online.
Drug–Protein interaction prediction by correcting the effect of incomplete information in heterogeneous information
Authors: Li Yanfei , Sun Chang , Wei Jin-Mao , Liu Jian
Published: September 2022

Motivation

Large-scale heterogeneous data provide diverse perspectives for predicting drug–protein interactions (DPIs). However, the available information on molecular interactions and clinical associations related to drugs or proteins is incomplete because there may be unproven interactions and associations. This incomplete information in the available data is presented in the form of non-interaction and non-correlation, which may mislead the prediction model. Existing methods fuse incomplete and complete information without considering their integrity, so the negative effects of incomplete information still exist.

Results

We develop a network-based DPI prediction method named BRWCP, which uses the complete information network to correct the prediction results acquired by the incomplete information network. By integrating relevant heterogeneous information that may be incomplete, the feature similarities of drugs and proteins are obtained. Combining the feature similarities and known DPIs, an incomplete information-based drug–protein heterogeneous network is constructed. Then, a bidirectional random walk with pruning algorithm is adopted in this heterogeneous network to predict potential DPIs. Next, the predicted DPIs are combined with the chemical fingerprint similarity of drugs and amino acid sequence similarity of proteins to construct the complete information network. The bidirectional random walk with pruning algorithm is applied in the new network to obtain the final prediction results until it converges. Experimental results show that BRWCP is superior to several state-of-the-art DPI prediction methods, and case studies further confirm its ability to tap potential DPIs.

Availability and implementation

The code and data used in BRWCP are available at https://github.com/lyfdomain/BRWCP.

Supplementary information

Supplementary data are available at Bioinformatics online.
Race and Men’s Imprisonment in the United States: Religious Conservatism, Political Conservatism and Racial Threat
Authors: Levchak Philip J , Heimer Karen , Lang Joseph B , Lauritsen Janet L
Published: September 2022

Black men are overrepresented in United States prisons and the number of Black men incarcerated increased dramatically during America’s “prison boom.” Yet, existing research on male imprisonment rates in the United States has focused on explaining overall rates and has not statistically modeled rates disaggregated by race over time. This study uses seemingly unrelated regression techniques to analyze annual rates of Black and non-Black men incarcerated in state prisons during the period of greatest increase in United States imprisonment rates. The findings show that increasing evangelical religious conservativism is associated with higher Black imprisonment rates and, importantly, this effect is “amplified” when state legislatures are more politically conservative. We also find that as Black populations increase, the punitive effect of religious conservatism is moderated or attenuated, and this holds for the incarceration of Black as well as non-Black men. In addition, consistent with a racial threat perspective, growth in Black populations in states is linked with increases in Black as well as non-Black male imprisonment rates. Together these effects emphasize the importance of examining imprisonment rates disaggregated by race and highlight the joint and conditional effects of religious conservatism, political conservatism, and racial threat for understanding imprisonment in the United States.
Professional Encounters with ‘the Other’: Widening Accessibility of Social Work Practices in Urban Neighbourhoods
Authors: Ponzoni Elena , de Ruyter Doret
Published: September 2022

Social work professionals in urban contexts struggle to serve different groups equally. Critical social work literature advocates critical reflexivity in social work practices. Focusing on existing support practices, it encourages scrutinising the implicit ways social work practices can maintain and reproduce power imbalances and othering structures. However, it has not examined the tensions connected with phases in which the first contact between clients and professionals occurs and clients’ engagement in social work programmes begins. Stimulated by an empirical research into parenting-support in a city in the Netherlands, this article examines theoretically the notion of ‘encounter practices’ through which professionals reach out to people considered in need of support but not asking for help. We disentangle how encounter practices can be interpreted through different understandings of professional engagement, emerging from either critical or affirmative traditions of social work. The encounter context poses specific challenges for critical reflexivity, but it also offers the possibility of exploring one’s social positioning in relation to others through informal micro-interactions preceding the instalment of professional relations between professionals and parents. Drawing on insights from urban studies, we distinguish ‘fleeting’, ‘convivial’ and ‘engaged encounters’ as different levels of encounter that allow unsettling othering structures in outreach practices.
Why are you just watching?: polyvalent Korean spectatorship and critical Western spectatorship in Squid Game
Authors: Dunn Jennifer C , Young Stephanie L
Published: September 2022

Although the narrative of Squid Game critiques socioeconomic structures, the characters, genre, filming techniques, and aesthetics, ironically, situate audiences as passive spectators. In this article, we discuss the ways Squid Game constructs a polyvalent Korean spectatorship and a critical Western spectatorship within the survival game genre. We argue the series hails spectators to consent to the same oppressive socioeconomic structures the show seemingly critiques. Additionally, we consider potentials of rhetorical witnessing for activating audiences and extending spectatorship theory.
Zonulin, as a marker of intestinal permeability, is elevated in IgA nephropathy and IgA vasculitis with nephritis
Authors: Li Qianqian , Yuan Xiaohan , Shi Sufang , Liu Lijun , Lv Jicheng , Zhu Li , Zhang Hong
Published: September 2022

Background

Immunoglobulin A nephropathy (IgAN) and IgA vasculitis with nephritis (IgAV-N) are considered related diseases and share some similar clinicopathologic phenotypes. Elevated circulating galactose-deficient IgA1 (Gd-IgA1)-containing immune complexes and mucosal immunity were associated with the pathogenesis of IgAN and IgAV-N. Recently, studies have identified that the zonulin level, as a modulator of intestinal permeability, is significantly elevated in several inflammatory and autoimmune-related diseases. However, whether zonulin also plays a role in IgAN and IgAV-N is not clear.

Methods

A total of 73 IgAV-N patients, 68 IgAN patients and 54 healthy controls were assessed for circulating zonulin and Gd-IgA1 levels by enzyme-linked immunosorbent assay. The diagnostic efficiency of the combination of zonulin with Gd-IgA1 was evaluated by the area under the receiver operating characteristic curve (AUC) and integrated discrimination improvement (IDI) analysis.

Results

Compared with healthy controls, we found that both IgAV-N and IgAN patients had elevated zonulin and Gd-IgA1 levels (P < .001). Additionally, patients with IgAV-N presented with even higher circulating zonulin levels than patients with IgAN (P = .020). The addition of zonulin to Gd-IgA1 showed better predictive performance than Gd-IgA1 alone in the diagnosis of both IgAN and IgAV-N, as illustrated by a significantly increased AUC (IgAN: 0.805 versus 0.708, P = .0021; IgAV-N: 0.886 versus 0.673, P < .001) and significant IDI (IgAN: IDI 0.136, P < .001; IgAV-N: IDI 0.281, P < .001).

Conclusion

Elevated circulating zonulin levels were detected in both patients with IgAV-N and those with IgAN. Combined detection of circulating zonulin and Gd-IgA1 is recommended as a noninvasive diagnostic biomarker for IgAV-N and IgAN.
DNA metabarcoding the diet of Podarcis lizards endemic to the Balearic Islands
Authors: Alemany Iris , Pérez-Cembranos Ana , Pérez-Mellado Valentín , Castro José Aurelio , Picornell Antònia , Ramon Cori , Jurado-Rivera José A
Published: September 2022

Dietary studies are essential to unravel the functioning of ecosystems and ultimately to understand biodiversity. This task, which at first may seem simple, becomes especially complex in those cases of omnivorous species with highly variable diets. In this regard, the emergence of next-generation DNA sequencing methodologies represents a powerful tool to address the problem. Here we implement a high-throughput metabarcoding strategy based on the analysis of four molecular markers aimed at sequencing both mitochondrial (animal prey) and chloroplast (diet plants) genome fragments from fecal samples of two lizard species endemic to the Balearic Archipelago (Podarcis lilfordi and P. pityusensis) obtained through non-invasive methods. The results allowed for the characterization of their diets with a high degree of taxonomic detail and have contributed a large number of new trophic records. The reported diets are based mainly on the consumption of arthropods, mollusks and plants from a diversity of taxonomic orders, as well as carrion and marine subsidies. Our analyses also reveal inter- and intra-specific differences both in terms of seasonality and geographical distribution of the sampled lizard populations. These molecular findings provide new insights into the trophic interactions of these threatened endemic lizards in their unique and isolated ecosystems.
TFLink: an integrated gateway to access transcription factor–target gene interactions for multiple species
Authors: Liska Orsolya , Bohár Balázs , Hidas András , Korcsmáros Tamás , Papp Balázs , Fazekas Dávid , Ari Eszter
Published: September 2022

Analysis of transcriptional regulatory interactions and their comparisons across multiple species are crucial for progress in various fields in biology, from functional genomics to the evolution of signal transduction pathways. However, despite the rapidly growing body of data on regulatory interactions in several eukaryotes, no databases exist to provide curated high-quality information on transcription factor–target gene interactions for multiple species. Here, we address this gap by introducing the TFLink gateway, which uniquely provides experimentally explored and highly accurate information on transcription factor–target gene interactions (∼12 million), nucleotide sequences and genomic locations of transcription factor binding sites (∼9 million) for human and six model organisms: mouse, rat, zebrafish, fruit fly, worm and yeast by integrating 10 resources. TFLink provides user-friendly access to data on transcription factor–target gene interactions, interactive network visualizations and transcription factor binding sites, with cross-links to several other databases. Besides containing accurate information on transcription factors, with a clear labelling of the type/volume of the experiments (small-scale or high-throughput), the source database and the original publications, TFLink also provides a wealth of standardized regulatory data available for download in multiple formats. The database offers easy access to high-quality data for wet-lab researchers, supplies data for gene set enrichment analyses and facilitates systems biology and comparative gene regulation studies.

Database URL https://tflink.net/
Re-intervention percutaneous balloon mitral valvuloplasty in a patient with left atrial appendage thrombus: a case report
Authors: Parikh Rujuta , Singh Gaurav , Mishra Ashish , Sharma Kamal
Published: September 2022

Background

Percutaneous balloon mitral valvuloplasty (PBMV) using an Accura balloon is an effective method for management of rheumatic mitral stenosis.

Case summary

Herein, we present a case of a 43-year-old female, who had undergone a previous PBMV, who presented with very severe mitral re-stenosis with Type Ia left atrial (LA) clot, in atrial fibrillation and New York Heart Association functional Class III. We used the modified septal puncture and over-the-wire technique, avoiding inadvertent manipulation of the LA clot for PBMV. The mitral valve was successfully dilated from 0.9 to 1.5 cm2, and the patient had an uneventful post-procedure recovery.

Discussion

The presence of LA clot and mitral re-stenosis in a previously intervened valve are considered unfavourable characteristics for a PBMV procedure, and patients are usually advised surgical intervention. These patients are also high-risk candidates for surgery due to late presentation with advanced disease and poor functional capacity. Our patient underwent successful re-intervention with PBMV despite having suboptimal characteristics.
Concrete proof of Murphy’s law: a case report of intracardiac cement embolization
Authors: Krithika Ramaprabhu , Geske Jeffrey B , Villarraga Hector R , Crestanello Juan
Published: September 2022

Background

The literature describing the complications following kyphoplasty is limited. This case report is a reminder that novel therapeutic strategies can be associated with unexpected complications.

Case summary

A 61-year-old woman with rheumatoid arthritis and degenerative lumbar disc disease underwent open posterior instrumented fusion with bilateral open L2 vertebroplasty elsewhere. A month after discharge, she presented to our institution with acute chest pain and dyspnoea. A subsequent gated cardiac computed tomography (CT) angiogram showed three distinct cardiopulmonary emboli. One of the cement fragments had perforated the inferior wall of the right ventricle close to the base of the posterior tricuspid valve leaflet with a moderate circumferential pericardial effusion. Operative extraction of multiple cement emboli as well as repair of the tricuspid valve was pursued. Postoperative echocardiogram showed trivial tricuspid regurgitation after repair. The patient had an uneventful postoperative course and was discharged from the hospital on postoperative Day 5.

Discussion

Cement embolization following kyphoplasty can be associated with serious complications such as vascular injury, hypoxaemia, pulmonary artery obstruction, and cardiac perforation. Clinicians must maintain a high index of suspicion as cement embolism may not always present acutely.
Systematic approach to outcome assessment from coded electronic healthcare records in the DaRe2THINK NHS-embedded randomized trial
Authors: Wang Xiaoxia , Mobley Alastair R , Tica Otilia , Okoth Kelvin , Ghosh Rebecca E , Myles Puja , Williams Tim , Haynes Sandra , Nirantharakumar Krishnarajah , Shukla David , Kotecha Dipak ,   the DaRe2THINK Trial Committees, Beatty Susan , Mehta Samir , Breeze Sophie , Lancaster Karen , Fordyce Stuart , Allen Naomi , Calvert Melanie , Denniston Alastair , Gkoutos George , Jayawardana Sahan , Ball Simon , Baigent Colin , Brocklehurst Peter , Lester Will , McManus Richard , Seri Stefano , Valentine Janet , Camm A John , Haynes Sandra , Moore Dame Julie , Rogers Amy , Stanbury Mary , Flather Marcus , Walker Suzy , Wang Duolao
Published: September 2022

Aims

Improving the efficiency of clinical trials is key to their continued importance in directing evidence-based patient care. Digital innovations, in particular the use of electronic healthcare records (EHRs), allow for large-scale screening and follow up of participants. However, it is critical these developments are accompanied by robust and transparent methods that can support high-quality and high clinical value research.

Methods and results

The DaRe2THINK trial includes a series of novel processes, including nationwide pseudonymized pre screening of the primary-care EHR across England, digital enrolment, remote e-consent, and ‘no-visit’ follow up by linking all primary- and secondary-care health data with patient-reported outcomes. DaRe2THINK is a pragmatic, healthcare-embedded randomized trial testing whether earlier use of direct oral anticoagulants in patients with prior or current atrial fibrillation can prevent thromboembolic events and cognitive decline (www.birmingham.ac.uk/dare2think). This study outlines the systematic approach and methodology employed to define patient information and outcome events. This includes transparency on all medical code lists and phenotypes used in the trial across a variety of national data sources, including Clinical Practice Research Datalink Aurum (primary care), Hospital Episode Statistics (secondary care), and the Office for National Statistics (mortality).

Conclusion

Co-designed by a patient and public involvement team, DaRe2THINK presents an opportunity to transform the approach to randomized trials in the setting of routine healthcare, providing high-quality evidence generation in populations representative of the community at risk.