bluuebunny/crossref_metadata_2025 huggingface dataset:
Permanence of equilibrium points in the basin of attraction and existence of periodic solutions for autonomous measure differential equations and dynamic equations on time scales via generalized ODEs
Authors: Federson M , Grau R , Mesquita J G , Toon E
Published: June 2022

It is well-known that generalized ODEs encompass several types of differential equations as, for instance, functional differential equations, measure differential equations, dynamic equations on time scales, impulsive differential equations and any combinations among them, not to mention integrals equations, among others. The aim of this paper is to establish a theory of autonomous equations in the setting of generalized ODEs. Thus, we introduce the notion of autonomous generalized ODEs as well as new classes of right-hand sides for nonautonomous generalized ODEs. Amongst the main results, we prove that one of these new classes coincide with the original class of right-hand sides introduced by Kurzweil in 1957. We also prove that autonomous generalized ODEs do not enlarge the class of autonomous ODEs with uniformly continuous right-hand sides. Motivated by this fact, we then enlarge the class of autonomous generalized ODEs so that discontinuities can be taken into account. We then introduce a more general class of autonomous generalized ODEs, in whose integral form, a Stieltjes-type integral appears. A correspondence between these equations and autonomous measure differential equations is established and several results are obtained. We mention local existence and uniqueness of solutions, continuous dependence of solutions on initial values, existence of periodic solutions and permanence of asymptotically stable equilibrium point in the basin of attraction. All these results are, then, specified not only for autonomous generalized ODEs, but also for autonomous measure differential equations and dynamic equations on time scales.
On spectral structure and spectral eigenvalue problems for a class of self similar spectral measure with product form
Authors: Li Jinjun , Wu Zhiyi
Published: June 2022

Let μ be a Borel probability measure with compact support on

R

d

. We say that μ is a spectral measure if there exists

Λ
⊆

R

d

, called a spectrum of μ, such that

E

(

Λ

)

≔

{

e

−
2
π
i

⟨

λ
,
x

⟩

}

λ
∈
Λ

forms an orthonormal basis for L
2(μ). In this paper, we study the structure of spectra for a class of self-similar spectral measure μ

R,B
with product form on

R

. We first give a partially characterize for E
Λ to be a maximal orthogonal family in L
2(μ

R,B
) by using the notion of maximal tree mapping. Based on this, we give a sufficient condition for a maximal orthogonal family E
Λ (which corresponds to a maximal tree mapping) to be an orthonormal basis of L
2(μ

R,B
). Moreover, we completely settle two types of spectral eigenvalue problems for μ

R,B
. Precisely, on the first case, for the model spectrum (simplest spectrum) of μ

R,B
, we characterize all possible real numbers t such that tΛ is also a spectrum of μ

R,B
. On the other case, we characterize all possible real numbers t such that there exists a countable set Λ such that Λ and tΛ are both spectra of μ

R,B
.
Corrigendum: Forward boundedness of the trace map for the period doubling substitution (2020 Nonlinearity

33 4390)
Authors: Carvalho T O
Published: June 2022

In a recent paper, Liu, Qu and Yao uncovered energies in the spectrum of the period doubling Hamiltonian whose trace map iterations go to infinity, in contrast with our results.
Elliptic flowers: simply connected billiard tables where chaotic (non-chaotic) flows move around chaotic (non-chaotic) cores
Authors: Bunimovich Leonid A
Published: June 2022

We introduce a class of billiards with chaotic unidirectional flows (or non-chaotic unidirectional flows with ‘vortices’) which go around a chaotic or non-chaotic ‘core’, where orbits can change their orientation. Moreover, the corresponding billiard tables are simply connected in difference with many attempts to build billiards with interesting and/or exotic dynamics by putting inside billiard tables various ‘scatterers’ with funny shapes. Therefore the billiards in this new class are amenable to experimental studies in physics labs as well as to the rigorous mathematical ones, which may shed a new light on understanding of classical and quantum dynamics of Hamiltonian systems.
Site selective 5f electronic correlations in β-uranium
Authors: Qiu Ruizhi , Xie Liuhua , Huang Li
Published: June 2022

We investigate the electronic structure of β-uranium, which has five nonequivalent atomic sites in its unit cell, by means of the density functional theory plus Hubbard-U correction with U from linear response calculation. It is found that the 5f electronic correlations in β-uranium are moderate. More interestingly, their strengths are site selective, depending on the local atomic environment of the present uranium atom. As a consequence, the occupation matrices and partial 5f density of states of β-uranium manifest site dependence. In addition, the complicate experimental structure of β-uranium could be well reproduced within this theoretical framework.
Data encryption based on a 9D complex chaotic system with quaternion for smart grid
Authors: Zhang Fangfang , Huang Zhe , Kou Lei , Li Yang , Cao Maoyong , Ma Fengying
Published: June 2022

With the development of smart grid, operation and control of a power system can be realized through the power communication network, especially the power production and enterprise management business involve a large amount of sensitive information, and the requirements for data security and real-time transmission are gradually improved. In this paper, a new 9-dimensional (9D) complex chaotic system with quaternion is proposed for the encryption of smart grid data. Firstly, we present the mathematical model of the system, and analyze its attractors, bifurcation diagram, complexity, and 0–1 test. Secondly, the pseudo-random sequences are generated by the new chaotic system to encrypt power data. Finally, the proposed encryption algorithm is verified with power data and images in the smart grid, which can ensure the encryption security and real time. The verification results show that the proposed encryption scheme is technically feasible and available for power data and image encryption in smart grid.
Modulated spatial transmission signals in the photonic bandgap
Authors: Xu Wenqi , Wang Hui , Xie Daohong , Che Junling , Zhang Yanpeng
Published: June 2022

This paper describes the spatial transmission of electromagnetically induced transparency and four-wave mixing signals in the photonic bandgap structure, which are modulated using the adjustable parameters of light fields. The spatial transmission patterns of the relevant signals are experimentally investigated with respect to the optical nonlinear Kerr effect that occurs in the modulation process. The experimental results reveal the spatial transmission patterns of the probe transmission and the four-wave mixing signals, such as focusing, defocusing, shifting, and spatial splitting. This study explains how the tunable parameters of light fields and their interactions with each other can regulate the spatial transmission of the light fields by changing the refractive indices of media, which provides a new research perspective and a degree of experimental technology support for more efficient all-optical communications.
Brain–computer interface-based action observation combined with peripheral electrical stimulation enhances corticospinal excitability in healthy subjects and stroke patients
Authors: Kim Min Gyu , Lim Hyunmi , Lee Hye Sun , Han In Jun , Ku Jeonghun , Kang Youn Joo
Published: June 2022

Objective. Action observation (AO) combined with brain–computer interface (BCI) technology enhances cortical activation. Peripheral electrical stimulation (PES) increases corticospinal excitability, thereby activating brain plasticity. To maximize motor recovery, we assessed the effects of BCI-AO combined with PES on corticospinal plasticity. Approach. Seventeen patients with chronic hemiplegic stroke and 17 healthy subjects were recruited. The participants watched a video of repetitive grasping actions with four different tasks for 15 min: (A) AO alone; (B) AO + PES; (C) BCI-AO + continuous PES; and (D) BCI-AO + triggered PES. PES was applied at the ulnar nerve of the wrist. The tasks were performed in a random order at least three days apart. We assessed the latency and amplitude of motor evoked potentials (MEPs). We examined changes in MEP parameters pre-and post-exercise across the four tasks in the first dorsal interosseous muscle of the dominant hand (healthy subjects) and affected hand (stroke patients). Main results. The decrease in MEP latency and increase in MEP amplitude after the four tasks were significant in both groups. The increase in MEP amplitude was sustained for 20 min after tasks B, C, and D in both groups. The increase in MEP amplitude was significant between tasks A vs. B, B vs. C, and C vs. D. The estimated mean difference in MEP amplitude post-exercise was the highest for A and D in both groups. Significance. The results indicate that BCI-AO combined with PES is superior to AO alone or AO + PES for facilitating corticospinal plasticity in both healthy subjects and patients with stroke. Furthermore, this study supports the idea that synchronized activation of cortical and peripheral networks can enhance neuroplasticity after stroke. We suggest that the BCI-AO paradigm and PES could provide a novel neurorehabilitation strategy for patients with stroke.
Coalescence of two branch points in complex time marks the end of rapid adiabatic passage and the start of Rabi oscillations
Authors: Kaprálová-Žďánská Petra Ruth , Šindelka Milan , Moiseyev Nimrod
Published: June 2022

We study theoretically the population transfer in two-level atoms driven by chirped lasers. It is known that in the Hermitian case, the rapid adiabatic passage (RAP) is stable for an above-critical chirp below which the final populations of states Rabi oscillate with varying laser power. We show that if the excited state is represented by a resonance, the separatrix marking this critical phenomenon in the space of the laser pulse parameters emanates from an exceptional point (EP)—a non-Hermitian singularity formed in the atomic system by the fast laser field oscillations and encircled due to slow variations of the laser pulse envelope and instantaneous frequency. This critical phenomenon is neatly understood via extending the ‘slow’ time variable into the complex plane, uncovering a set of branch points which encode non-adiabatic dynamics, where the switch between RAP and Rabi oscillations is triggered by a coalescence of two such branch points. We assert that the intriguing interrelation between the two different singularities—the EP and the branch point coalescence in complex time plane—can motivate feasible experiments involving laser driven atoms.
Effect of chemical-heat treatment on the properties of titanium
Authors: Bricín D , Kratochvílová L , Leták R , Vojta L , Nová K , Špirit Z
Published: June 2022

The aim of this study is to evaluate the properties and microstructure of pure titanium after its chemical heat treatment (CHT) by boriding and nitriding. Nitriding and boriding were both done in powder backfill for ten hours. The temperature of the nitriding was 550 °C. The temperature of the boriding was 1000 °C. Both processes led to the creation of a thin surface layer of nitrides and borides which affected wear resistance and also they affected corrosion resistance of the surface of the analyzed samples.
Differential-phase-shift quantum digital signature without disclosing measurement information
Authors: Inoue Kyo , Honjo Toshimori
Published: June 2022

A novel quantum digital signature (QDS) scheme using differential-phase-shift signal is presented. A sender broadcasts a weak coherent pulse train with 0 or π phase to receivers, who measure its relative phases using delay interferometers with photon detectors and then employ the measurement results as authentication keys. The key distribution stage is completed with this signal transmission. Neither exchange of basis information between the sender and receivers nor exchange of a portion of a sifted key between the receivers with each other are conducted, unlike conventional QDS protocols. Therefore, our system is simpler than conventional ones. The security of the proposed scheme is discussed, and calculations evaluating system parameters to guarantee the QDS operation, such as the key length and authentication threshold, are presented.
Optimized two-step second derivative methods for the solutions of stiff systems
Authors: Sunday Joshua
Published: June 2022

In this research article, a pair of optimized two-step second derivative methods is derived and implemented on stiff systems. The influence of equidistant and non-equidistant hybrid points spacing on the performance of the methods derived is investigated. Firstly, the methods are derived using interpolation and collocation of a finite power series at some selected grid points. This leads to the formation of a system of nonlinear equations, which are then solved for the unknown parameters to obtain a continuous second derivative scheme. The by-products of the evaluation of the continuous second derivative scheme lead to the development of discrete methods in the form of blocks. Secondly, the basic properties of the methods derived were analysed. Numerical results were generated to investigate the influence of equidistant and non-equidistant hybrid points spacing on the performance of the methods on stiff systems. The results so obtained clearly showed that the two-step second derivative method with equidistant hybrid point spacing performed better than the two-step second derivative method with non-equidistant hybrid point spacing. This implies that equidistant hybrid point spacing enhances the accuracy of a method as opposed to non-equidistant hybrid point spacing.
Reduction in reversal of global stilling arising from correction to encoding of calm periods
*
Authors: Dunn Robert J H , Azorin-Molina Cesar , Menne Matthew J , Zeng Zhenzhong , Casey Nancy W , Shen Cheng
Published: June 2022

We describe an undocumented change in how calm periods in near-surface wind speed (and direction) observations have been encoded in a subset of global datasets of sub-daily data after 2013. This has resulted in the under-estimation of the number of calm periods for meteorological stations across much of Asia and Europe. Hence average wind speeds after 2013 have been over-estimated, affecting the assessment of changes in global stilling and reversal phenomena after this date. By addressing this encoding change we show that globally, since 2010, wind speeds have recovered by around 30% less than previously thought.
Minimizing environmental impacts of solar farms: a review of current science on landscape hydrology and guidance on stormwater management
Authors: Yavari Rouhangiz , Zaliwciw Demetrius , Cibin Raj , McPhillips Lauren
Published: June 2022

As solar energy becomes an increasingly cheap source of renewable energy, major utility-scale ground solar panel installations, often called ‘solar farms’, are rapidly growing. With these solar farms often covering hundreds of acres, there is the potential for impacts on natural hydrologic processes, including runoff generation and erosion. Here we review the current state of scientific research on the hydrology and water quality impacts of solar farms, as well as management recommendations for minimizing any impacts. The limited field measurements indicate the redistribution of soil moisture around solar farms, but the net impacts on runoff and erosion are less clear. Research focused on coupling solar farms with agriculture as ‘agrivoltaics’ demonstrates reduced evaporative water losses and associated crop stress, particularly in more arid regions. With regards to land and the stormwater management associated with solar farms, most US states currently do not have solar farm-specific recommendations and instead defer to standard stormwater management permits and guidance. In states with solar farm-specific guidance, typical recommendations include minimizing construction-related compaction, ensuring a high cover of perennial vegetation with minimal maintenance, and designing with pervious space between solar panel rows to promote infiltration of any runoff; in some cases, structural stormwater management like infiltration basins may be required. In general, solar farms can be designed to minimize the impact on landscape ecohydrological processes, but more research is needed to determine whether current recommendations are adequate. In particular, there is a need for more field research on less ideal sites such as those with higher slopes.
An effective clean energy transition must anticipate growing climate disruptions
Authors: Lesk Corey , Kornhuber Kai
Published: June 2022

As the clean energy transition gathers momentum, it will face myriad technical, economic, and political challenges. However, one in particular is often underappreciated: the potential disruption to the transition from surging climate extremes. We identify three ways in which extreme events may impede the transition: direct physical impacts to transitional infrastructure, strained resources due to rising recovery costs, and political backlash from disaster-affected populations. If these pitfalls materialize, the transition could stall, leading to continued emissions, additional worsening of climate extremes, and further disruption of the transition. We propose three avenues to avoid this potential positive feedback: integration of adaptation and mitigation as mutually supportive goals, fostering political and cultural commitment to a sustained transition, and an interdisciplinary research and training agenda to improve modeling and preparedness for the cascading impacts of climate extremes
An algorithm for Hodge ideals
Authors: Blanco Guillem
Published: June 2022

We present an algorithm to compute the Hodge ideals (see M. Mustaţă and M. Popa [Mem. Amer. Math. Soc. 262 (2019), pp. v + 80; J. Éc. polytech. Math. 6 (2019), pp. 283–328]) of

Q

\mathbb {Q}

-divisors associated to any reduced effective divisor

D
D

. The computation of the Hodge ideals is based on an algorithm to compute parts of the

V
V

-filtration of Kashiwara and Malgrange on

ι

+

O

X

(
∗
D
)

\iota _{+}\mathscr {O}_X(*D)

and the characterization (see M. Mustaţă and M. Popa [Forum Math. Sigma 8 (2020), p. 41]) of the Hodge ideals in terms of this

V
V

-filtration. In particular, this gives a new algorithm to compute the multiplier ideals and the jumping numbers of any effective divisor.
A fully discrete plates complex on polygonal meshes with application to the Kirchhoff–Love problem
Authors: Di Pietro Daniele , Droniou Jérôme
Published: June 2022

In this work we develop a novel fully discrete version of the plates complex, an exact Hilbert complex relevant for the mixed formulation of fourth-order problems. The derivation of the discrete complex follows the discrete de Rham paradigm, leading to an arbitrary-order construction that applies to meshes composed of general polygonal elements. The discrete plates complex is then used to derive a novel numerical scheme for Kirchhoff–Love plates, for which a full stability and convergence analysis are performed. Extensive numerical tests complete the exposition.
The non-tangential boundary behavior of the matrix-valued rational inner functions on bounded symmetric domain
Authors: Wang Kai , Zhang Shuyi
Published: June 2022

Knese [Proc. LMS 111(2015), 1261-1306] proved every rational inner function on polydisc has a non-tangential limit at every point of the Shilov boundary. We extended his result to the case of functions on general bounded symmetric domains. Namely, every rational inner function on a bounded symmetric domain has a non-tangential limit of modulus11at every point of the Shilov boundary. We also prove that every matrix-valued rational inner function on tube-type domain has a unitary non-tangential limit at every point of the Shilov boundary.
HyperGraphs.jl: representing higher-order relationships in Julia
Authors: Diaz Léo P M , Stumpf Michael P H
Published: June 2022

HyperGraphs.jl is a Julia package that implements hypergraphs. These are a generalization of graphs that allow us to represent n-ary relationships and not just binary, pairwise relationships. High-order interactions are commonplace in biological systems and are of critical importance to their dynamics; hypergraphs thus offer a natural way to accurately describe and model these systems.

Availability and implementation

HyperGraphs.jl is freely available under the MIT license. Source code and documentation can be found at https://github.com/lpmdiaz/HyperGraphs.jl.

Supplementary information

Supplementary data are available at Bioinformatics online.
Prediction of allosteric communication pathways in proteins
Authors: Haliloglu Turkan , Hacisuleyman Aysima , Erman Burak
Published: June 2022

Motivation

Allostery in proteins is an essential phenomenon in biological processes. In this article, we present a computational model to predict paths of maximum information transfer between active and allosteric sites. In this information theoretic study, we use mutual information as the measure of information transfer, where transition probability of information from one residue to its contacting neighbors is proportional to the magnitude of mutual information between the two residues. Starting from a given residue and using a Hidden Markov Model, we successively determine the neighboring residues that eventually lead to a path of optimum information transfer. The Gaussian approximation of mutual information between residue pairs is adopted. The limits of validity of this approximation are discussed in terms of a nonlinear theory of mutual information and its reduction to the Gaussian form.

Results

Predictions of the model are tested on six widely studied cases, CheY Bacterial Chemotaxis, B-cell Lymphoma extra-large (Bcl-xL), Human proline isomerase cyclophilin A (CypA), Dihydrofolate reductase (DHFR), HRas GTPase and Caspase-1. The communication transmission rendering the propagation of local fluctuations from the active sites throughout the structure in multiple paths correlate well with the known experimental data. Distinct paths originating from the active site may likely represent a multi functionality such as involving more than one allosteric site and/or pre-existence of some other functional states. Our model is computationally fast and simple and can give allosteric communication pathways, which are crucial for the understanding and control of protein functionality.

Supplementary information

Supplementary data are available at Bioinformatics online.
Deep learning for survival analysis in breast cancer with whole slide image data
Authors: Liu Huidong , Kurc Tahsin
Published: June 2022

Motivation

Whole slide tissue images contain detailed data on the sub-cellular structure of cancer. Quantitative analyses of this data can lead to novel biomarkers for better cancer diagnosis and prognosis and can improve our understanding of cancer mechanisms. Such analyses are challenging to execute because of the sizes and complexity of whole slide image data and relatively limited volume of training data for machine learning methods.

Results

We propose and experimentally evaluate a multi-resolution deep learning method for breast cancer survival analysis. The proposed method integrates image data at multiple resolutions and tumor, lymphocyte and nuclear segmentation results from deep learning models. Our results show that this approach can significantly improve the deep learning model performance compared to using only the original image data. The proposed approach achieves a c-index value of 0.706 compared to a c-index value of 0.551 from an approach that uses only color image data at the highest image resolution. Furthermore, when clinical features (sex, age and cancer stage) are combined with image data, the proposed approach achieves a c-index of 0.773.

Availability and implementation

https://github.com/SBU-BMI/deep_survival_analysis
WAT3R: recovery of T-cell receptor variable regions from 3′ single-cell RNA-sequencing
Authors: Ainciburu Marina , Morgan Duncan M , DePasquale Erica A K , Love J Christopher , Prósper Felipe , van Galen Peter
Published: June 2022

Diversity of the T-cell receptor (TCR) repertoire is central to adaptive immunity. The TCR is composed of α and β chains, encoded by the TRA and TRB genes, of which the variable regions determine antigen specificity. To generate novel biological insights into the complex functioning of immune cells, combined capture of variable regions and single-cell transcriptomes provides a compelling approach. Recent developments enable the enrichment of TRA and TRB variable regions from widely used technologies for 3′-based single-cell RNA-sequencing (scRNA-seq). However, a comprehensive computational pipeline to process TCR-enriched data from 3′ scRNA-seq is not available. Here, we present an analysis pipeline to process TCR variable regions enriched from 3′ scRNA-seq cDNA. The tool reports TRA and TRB nucleotide and amino acid sequences linked to cell barcodes, enabling the reconstruction of T-cell clonotypes with associated transcriptomes. We demonstrate the software using peripheral blood mononuclear cells from a healthy donor and detect TCR sequences in a high proportion of single T cells. Detection of TCR sequences is low in non-T-cell populations, demonstrating specificity. Finally, we show that TCR clones are larger in CD8 Memory T cells than in other T-cell types, indicating an association between T-cell clonotypes and differentiation states.

Availability and implementation

The Workflow for Association of T-cell receptors from 3′ single-cell RNA-seq (WAT3R), including test data, is available on GitHub (https://github.com/mainciburu/WAT3R), Docker Hub (https://hub.docker.com/r/mainciburu/wat3r) and a workflow on the Terra platform (https://app.terra.bio). The test dataset is available on GEO (accession number GSE195956).

Supplementary information

Supplementary data are available at Bioinformatics online.
Effectiveness of the Ad26.COV2.S (Johnson & Johnson) Coronavirus Disease 2019 (COVID-19) Vaccine for Preventing COVID-19 Hospitalizations and Progression to High Disease Severity in the United States
Authors: Lewis Nathaniel M , Self Wesley H , Gaglani Manjusha , Ginde Adit A , Douin David J , Keipp Talbot H , Casey Jonathan D , Mohr Nicholas M , Zepeski Anne , Ghamande Shekhar A , McNeal Tresa A , Shapiro Nathan I , Gibbs Kevin W , Files D Clark , Hager David N , Shehu Arber , Prekker Matthew E , Erickson Heidi L , Gong Michelle N , Mohamed Amira , Johnson Nicholas J , Srinivasan Vasisht , Steingrub Jay S , Peltan Ithan D , Brown Samuel M , Martin Emily T , Monto Arnold S , Khan Akram , Busse Laurence W , Lohuis Caitlin C ten , Duggal Abhijit , Wilson Jennifer G , Gordon Alexandra June , Qadir Nida , Chang Steven Y , Mallow Christopher , Rivas Carolina , Babcock Hilary M , Kwon Jennie H , Exline Matthew C , Lauring Adam S , Halasa Natasha , Chappell James D , Grijalva Carlos G , Rice Todd W , Rhoads Jillian P , Jones Ian D , Stubblefield William B , Baughman Adrienne , Womack Kelsey N , Lindsell Christopher J , Hart Kimberly W , Zhu Yuwei , Adams Katherine , Patel Manish M , Tenforde Mark W ,   IVY Network Collaborators
Published: June 2022

Background . Adults in the United States (US) began receiving the adenovirus vector coronavirus disease 2019 (COVID-19) vaccine, Ad26.COV2.S (Johnson & Johnson [Janssen]), in February 2021. We evaluated Ad26.COV2.S vaccine effectiveness (VE) against COVID-19 hospitalization and high disease severity during the first 10 months of its use.

Methods . In a multicenter case-control analysis of US adults (≥18 years) hospitalized 11 March to 15 December 2021, we estimated VE against susceptibility to COVID-19 hospitalization (VEs), comparing odds of prior vaccination with a single dose Ad26.COV2.S vaccine between hospitalized cases with COVID-19 and controls without COVID-19. Among hospitalized patients with COVID-19, we estimated VE against disease progression (VEp) to death or invasive mechanical ventilation (IMV), comparing odds of prior vaccination between patients with and without progression.

Results . After excluding patients receiving mRNA vaccines, among 3979 COVID-19 case-patients (5% vaccinated with Ad26.COV2.S) and 2229 controls (13% vaccinated with Ad26.COV2.S), VEs of Ad26.COV2.S against COVID-19 hospitalization was 70% (95% confidence interval [CI]: 63–75%) overall, including 55% (29–72%) among immunocompromised patients, and 72% (64–77%) among immunocompetent patients, for whom VEs was similar at 14–90 days (73% [59–82%]), 91–180 days (71% [60–80%]), and 181–274 days (70% [54–81%]) postvaccination. Among hospitalized COVID-19 case-patients, VEp was 46% (18–65%) among immunocompetent patients.

Conclusions . The Ad26.COV2.S COVID-19 vaccine reduced the risk of COVID-19 hospitalization by 72% among immunocompetent adults without waning through 6 months postvaccination. After hospitalization for COVID-19, vaccinated immunocompetent patients were less likely to require IMV or die compared to unvaccinated immunocompetent patients.
Soluble Urokinase-Type Plasminogen Activator Receptor as a Prognostic Marker of Ugandan Children at Risk of Severe and Fatal Malaria
Authors: Stefanova Veselina , Ngai Michelle , Weckman Andrea M , Wright Julie K , Zhong Kathleen , Richard-Greenblatt Melissa , McDonald Chloe R , Conroy Andrea L , Namasopo Sophie , Opoka Robert O , Hawkes Michael , Kain Kevin C
Published: June 2022

Background

Current malaria diagnostic tests do not reliably identify children at risk of severe and fatal infection. Host immune and endothelial activation contribute to malaria pathogenesis. Soluble urokinase-type plasminogen activator receptor (suPAR) is a marker of these pathways. We hypothesized that measuring suPAR at presentation could risk-stratify children with malaria.

Methods

Plasma suPAR levels were determined in consecutive febrile children with malaria at presentation to hospital in Jinja, Uganda. We evaluated the accuracy of suPAR in predicting in-hospital mortality, and whether suPAR could improve a validated clinical scoring system (Lambaréné Organ Dysfunction Score [LODS]).

Results

Of the 1226 children with malaria, 39 (3.2%) died. suPAR concentrations at presentation were significantly higher in children who went on to die than in those who survived (P < .0001). suPAR levels were associated with disease severity (LODS: 0 vs 1, P = .001; 1 vs 2, P < .001; 2 vs 3, 0 vs 2, 1 vs 3, and 0 vs 3, P < .0001). suPAR concentrations were excellent predictors of in-hospital mortality (area under the receiver operating characteristic curve [AUROC], 0.92 [95% confidence interval {CI}, .91–.94]). The prognostic accuracy of LODS (AUROC, 0.93 [95% CI, .91–.94]) was improved when suPAR was added (AUROC, 0.97 [95% CI, .96–.98]; P < .0001).

Conclusions

Measuring suPAR at presentation can identify children at risk of severe and fatal malaria. Adding suPAR to clinical scores could improve the recognition and triage of children at risk of death. suPAR can be detected with a point-of-care test and can now be evaluated in prospective trials.
The Lanzhou Brucella Leak: The Largest Laboratory Accident in the History of Infectious Diseases?
Authors: Pappas Georgios
Published: June 2022

An inadequacy in sanitizing processes in a biopharmaceutical plant in Lanzhou, China, during July and August 2019, led to the aerosolization of Brucella that was subsequently spread through wind to nearby settlements and academic institutes, resulting in >10 000 human brucellosis cases, as of November 2020. The leak, possibly the largest laboratory accident in the history of infectious diseases, underlines the particular characteristics of Brucella that have made the pathogen a historical entity in biodefense research and a major cause of laboratory-associated infections. It further underlines the need for enhanced vigilance and strict regulatory interventions in similar facilities.
Direct and cross-generational effects of reproduction on fitness and behavioral variability in male-biased environments
Authors: Sanmartín-Villar Iago , Yu Xin , Cordero-Rivera Adolfo
Published: June 2022

Population structure determines individuals’ interactions and trade-offs with evolutionary consequences. Male-biased populations increase intrasexual competition and intersexual harassment, reducing female resource acquisition, and thus, resources availability for the following generation. We analyzed direct and cross-generational effects of male harassment in two generations of damselflies (Odonata). We exposed adult females to treatments with different sex-ratio and density (balanced and male-biased) to modify the male harassment level. We analyzed female fecundity, fertility, and number of faecal deposits as an indirect measure of resources acquisition. We studied female flight performance after repeated exposures to males. We analyzed survivorship, development, exploration, thigmotaxis, and feeding latency of larvae produced by the experimental females. In both generations, we analyzed four metrics of behavior: mean value, interindividual differences in plasticity, intra-individual unpredictability, and repeatability. Mating duration increased in male-biased treatment, whereas female resources acquisition and fertility decreased. Females that mated longer showed higher fecundity when they were exposed to balanced treatment, but not if they were exposed to male-biased treatment. Females from the male-biased treatment showed interindividual differences in plasticity and no repeatability in flight performance. Offspring showed balanced sex-ratio and similar survivorship, development, and feeding latency independently of the parental treatment; however, females exposed to male-biased treatment produced offspring with higher differences in exploration plasticity and daughters less explorative and with higher unpredictable thigmotaxis. We propose prolonged copulation as courtship at balanced sex-ratio but a cost to females under male-biased sex-ratio. Cross-generational effects in behavioral variability may be a mechanism to cope with predicted future environments.
Effects of omecamtiv mecarbil in heart failure with reduced ejection fraction according to blood pressure: the GALACTIC-HF trial
Authors: Metra Marco , Pagnesi Matteo , Claggett Brian L , Díaz Rafael , Felker G Michael , McMurray John J V , Solomon Scott D , Bonderman Diana , Fang James C , Fonseca Cândida , Goncalvesova Eva , Howlett Jonathan G , Li Jing , O’Meara Eileen , Miao Zi Michael , Abbasi Siddique A , Heitner Stephen B , Kupfer Stuart , Malik Fady I , Teerlink John R
Published: June 2022

Aim

Patients with heart failure with reduced ejection fraction and low systolic blood pressure (SBP) have high mortality, hospitalizations, and poorly tolerate evidence-based medical treatment. Omecamtiv mecarbil may be particularly helpful in such patients. This study examined its efficacy and tolerability in patients with SBP ≤100 mmHg enrolled in the Global Approach to Lowering Adverse Cardiac outcomes Through Improving Contractility in Heart Failure (GALACTIC-HF).

Methods and results

The GALACTIC-HF enrolled patients with baseline SBP ≥85 mmHg with a primary outcome of time to cardiovascular death or first heart failure event. In this analysis, patients were divided according to their baseline SBP (≤100 vs. >100 mmHg). Among the 8232 analysed patients, 1473 (17.9%) had baseline SBP ≤100 mmHg and 6759 (82.1%) had SBP >100 mmHg. The primary outcome occurred in 715 (48.5%) and 2415 (35.7%) patients with SBP ≤100 and >100 mmHg, respectively. Patients with lower SBP were at higher risk of adverse outcomes. Omecamtiv mecarbil, compared with placebo, appeared to be more effective in reducing the primary composite endpoint in patients with SBP ≤100 mmHg [hazard ratio (HR), 0.81; 95% confidence interval (CI), 0.70–0.94] compared with those with SBP >100 mmHg (HR, 0.95; 95% CI, 0.88–1.03; P-value for interaction = 0.051). In both groups, omecamtiv mecarbil did not change SBP values over time and did not increase the risk of adverse events, when compared with placebo.

Conclusion

In GALACTIC-HF, risk reduction of heart failure outcomes with omecamtiv mecarbil compared with placebo was large and significant in patients with low SBP. Omecamtiv mecarbil did not affect SBP and was well tolerated independent of SBP values.
Local adaptation in fungi
Authors: Bazzicalupo Anna
Published: June 2022

In this review, I explore the pervasive but underappreciated role of local adaptation in fungi. It has been difficult historically to study local adaptation in fungi because of the limited understanding of fungal species and their traits, but new hope has been offered with technological advances in sequencing. The filamentous nature of fungi invalidates some assumptions made in evolution because of their ability to exist as multinucleate entities with genetically different nuclei sharing the same cytoplasm. Many insights on local adaptation have come from studying fungi, and much of the empirical evidence gathered about local adaptation in the context of host–pathogen interactions comes from studying fungal virulence genes, drug resistance, and environmental adaptation. Together, these insights paint a picture of the variety of processes involved in fungal local adaptation and their connections to the unusual cell biology of Fungi (multinucleate, filamentous habit), but there is much that remains unknown, with major gaps in our knowledge of fungal species, their phenotypes, and the ways by which they adapt to local conditions.
Chromosomal-level reference genome assembly of the North American wolverine (Gulo gulo luscus): a resource for conservation genomics
Authors: Lok Si , Lau Timothy N H , Trost Brett , Tong Amy H Y , Wintle Richard F , Engstrom Mark D , Stacy Elise , Waits Lisette P , Scrafford Matthew , Scherer Stephen W
Published: June 2022

We report a chromosomal-level genome assembly of a male North American wolverine (Gulo gulo luscus) from the Kugluktuk region of Nunavut, Canada. The genome was assembled directly from long-reads, comprising: 758 contigs with a contig N50 of 36.6 Mb; contig L50 of 20; base count of 2.39 Gb; and a near complete representation (99.98%) of the BUSCO 5.2.2 set of 9,226 genes. A presumptive chromosomal-level assembly was generated by scaffolding against two chromosomal-level Mustelidae reference genomes, the ermine and the Eurasian river otter, to derive a final scaffold N50 of 144.0 Mb and a scaffold L50 of 7. We annotated a comprehensive set of genes that have been associated with models of aggressive behavior, a trait which the wolverine is purported to have in the popular literature. To support an integrated, genomics-based wildlife management strategy at a time of environmental disruption from climate change, we annotated the principal genes of the innate immune system to provide a resource to study the wolverine’s susceptibility to new infectious and parasitic diseases. As a resource, we annotated genes involved in the modality of infection by the coronaviruses, an important class of viral pathogens of growing concern as shown by the recent spillover infections by severe acute respiratory syndrome coronavirus-2 to naïve wildlife. Tabulation of heterozygous single nucleotide variants in our specimen revealed a heterozygosity level of 0.065%, indicating a relatively diverse genetic pool that would serve as a baseline for the genomics-based conservation of the wolverine, a rare cold-adapted carnivore now under threat.
Functional analysis of the N-terminal region of Vibrio FlhG, a MinD-type ATPase in flagellar number control
Authors: Homma Michio , Mizuno Akira , Hao Yuxi , Kojima Seiji
Published: June 2022

GTPase FlhF and ATPase FlhG are two key factors involved in regulating the flagellum number in Vibrio alginolyticus. FlhG is a paralogue of the Escherichia coli cell division regulator MinD and has a longer N-terminal region than MinD with a conserved DQAxxLR motif. The deletion of this N-terminal region or a Q9A mutation in the DQAxxLR motif prevents FlhG from activating the GTPase activity of FlhF in vitro and causes a multi-flagellation phenotype. The mutant FlhG proteins, especially the N-terminally deleted variant, were remarkably reduced compared to that of the wild-type protein in vivo. When the mutant FlhG was expressed at the same level as the wild-type FlhG, the number of flagella was restored to the wild-type level. Once synthesized in Vibrio cells, the N-terminal region mutation in FlhG seems not to affect the protein stability. We speculated that the flhG translation efficiency is decreased by N-terminal mutation. Our results suggest that the N-terminal region of FlhG controls the number of flagella by adjusting the FlhF activity and the amount of FlhG in vivo. We speculate that the regulation by FlhG, achieved through transcription by the master regulator FlaK, is affected by the mutations, resulting in reduced flagellar formation by FlhF.
Rapid and Efficient Detection by PCR ofCulicoides insignis(Diptera: Ceratopogonidae), the Main Vector of Bluetongue Virus (BTV) in the Neotropical Region
Authors: Ayala Mahia Mariel , Díaz Florentina , Micieli María Victoria , Spinelli Gustavo Ricardo , Ronderos María Marcela
Published: June 2022

Bluetongue virus (BTV) causes a viral, non-contagious disease that mainly affects sheep, cattle, and wild and farmed ruminants causing damage to these animals and significant economic losses. Culicoides insignis Lutz, the major BTV vector in South America, is one of the most abundant species in Argentina and commonly associated with cattle farms. The morphological identification of Culicoides spp. is routinely carried out with the aid of morphological keys, which mainly refer to the wing patterns, sensillae of palpi, and antennal flagella. Molecular tools applied to taxonomy provide a rapid and efficient method of identification of vector species. An easy protocol for the extraction of total DNA from single midges is herein described, and a forward primer for rapid and reliably test detection by polymerase chain reaction of C. insignis is developed.
Enzyme activity profiling for physiological phenotyping within functional phenomics: plant growth and stress responses
Authors: Jammer Alexandra , Akhtar Saqib Saleem , Amby Daniel Buchvaldt , Pandey Chandana , Mekureyaw Mengistu F , Bak Frederik , Roth Peter M , Roitsch Thomas
Published: June 2022

High-throughput profiling of key enzyme activities of carbon, nitrogen, and antioxidant metabolism is emerging as a valuable approach to integrate cell physiological phenotyping into a holistic functional phenomics approach. However, the analyses of the large datasets generated by this method represent a bottleneck, often keeping researchers from exploiting the full potential of their studies. We address these limitations through the exemplary application of a set of data evaluation and visualization tools within a case study. This includes the introduction of multivariate statistical analyses that can easily be implemented in similar studies, allowing researchers to extract more valuable information to identify enzymatic biosignatures. Through a literature meta-analysis, we demonstrate how enzyme activity profiling has already provided functional information on the mechanisms regulating plant development and response mechanisms to abiotic stress and pathogen attack. The high robustness of the distinct enzymatic biosignatures observed during developmental processes and under stress conditions underpins the enormous potential of enzyme activity profiling for future applications in both basic and applied research. Enzyme activity profiling will complement molecular -omics approaches to contribute to the mechanistic understanding required to narrow the genotype-to-phenotype knowledge gap and to identify predictive biomarkers for plant breeding to develop climate-resilient crops.
Neutrino observations of LHAASO sources: Present constraints and future prospects
Authors: Huang Tian-Qi , Li Zhuo
Published: June 2022

The Large High Altitude Air Shower Observatory (LHAASO) observed a dozen gamma-ray sources with significant emission above 100 TeV that may be strong candidates for PeVatrons. Neutrino observations are crucial for diagnosing whether the gamma-ray radiative process is hadronic or leptonic. We use the Bayesian method to analyse the 10-yr (2008–2018) IceCube data, and hence constrain the hadronic gamma-ray emission in the LHAASO sources. The present neutrino data show that the hadronic gamma-ray flux from the Crab Nebula is lower than the observed gamma-ray flux at the 90 per cent confidence level and contributes less than 86 per cent, which disfavours the hadronic origin of gamma-rays below tens of TeV. For the other LHAASO sources, the present neutrino observations cannot put useful constraints on the gamma-ray radiative process. We consider the uncertainty of the source extension: the upper limits on the hadronic gamma-ray flux tend to increase with the extension; and some sources, namely LHAASO J2032+4102, LHAASO J1929+1745, and LHAASO J1908+0621, show a relatively high statistical significance of neutrino signals if the extension is ≲ 0.°6. Finally, we estimate the future observational results of LHAASO sources by proposed neutrino telescopes. If the LHAASO-observed PeV gamma-rays are of hadronic origin, the Crab Nebula may be detected at >100 TeV at the 3σ confidence level within 20 years by a neutrino detector with an effective area 30 times that of IceCube.
Zeaxanthin Epoxidase Activity Is Downregulated by Hydrogen Peroxide
Authors: Holzmann Dimitrij , Bethmann Stephanie , Jahns Peter
Published: June 2022

The xanthophyll zeaxanthin (Zx) serves important photoprotective functions in chloroplasts and is particularly involved in the dissipation of excess light energy as heat in the antenna of photosystem II (PSII). Zx accumulates under high-light (HL) conditions in thylakoid membranes and is reconverted to violaxanthin by Zx epoxidase (ZEP) in low light or darkness. ZEP activity is completely inhibited under long-lasting HL stress, and the ZEP protein becomes degraded along with the PSII subunit D1 during photoinhibition of PSII. This ZEP inactivation ensures that high levels of Zx are maintained under harsh HL stress. The mechanism of ZEP inactivation is unknown. Here, we investigated ZEP inactivation by reactive oxygen species (ROS) under in vitro conditions. Our results show that ZEP activity is completely inhibited by hydrogen peroxide (H2O2), whereas inhibition by singlet oxygen or superoxide seems rather unlikely. Due to the limited information about the amount of singlet oxygen and superoxide accumulating under the applied experimental conditions, however, a possible inhibition of ZEP activity by these two ROS cannot be generally excluded. Despite this limitation, our data support the hypothesis that the accumulation of ROS, in particular H2O2, might be responsible for HL-induced inactivation of ZEP under in vivo conditions.