bluuebunny/crossref_metadata_2025 huggingface dataset:
Parental care results in a greater mutation load, for which it is also a phenotypic antidote
Authors: Pascoal Sonia , Shimadzu Hideyasu , Mashoodh Rahia , Kilner Rebecca M.
Published: May 2022

Benevolent social behaviours, such as parental care, are thought to enable mildly deleterious mutations to persist. We tested this prediction experimentally using the burying beetleNicrophorus vespilloides, an insect with biparental care. For 20 generations, we allowed replicate experimental burying beetle populations to evolve either with post-hatching care (‘Full Care’ populations) or without it (‘No Care’ populations). We then established new lineages, seeded from these experimental populations, which we inbred to assess their mutation load. Outbred lineages served as controls. We also tested whether the deleterious effects of a greater mutation load could be concealed by parental care by allowing half the lineages to receive post-hatching care, while half did not. We found that inbred lineages from the Full Care populations went extinct more quickly than inbred lineages from the No Care populations – but only when offspring received no post-hatching care. We infer that Full Care lineages carried a greater mutation load, but that the associated deleterious effects on fitness could be overcome if larvae received parental care. We suggest that the increased mutation load caused by parental care increases a population’s dependence upon care. This could explain why care is seldom lost once it has evolved.
A Self-Healing, Viscoelastic Hydrogel Promotes Healing of Brain Lesions
Authors: Hu Yan , Jia Yuanbo , Wang Siwei , Ma Yufei , Huang Guoyou , Ding Tan , Feng Dayun , Genin Guy M. , Wei Zhao , Xu Feng
Published: May 2022

Brain lesions can arise from traumatic brain injury, infection, and craniotomy. Although injectable hydrogels show promise for promoting healing of lesions and health of surrounding tissue, enabling cellular ingrowth and restoring neural tissue continue to be challenging. We hypothesized that these challenges arise in part from viscoelastic mismatch between the hydrogel and the brain parenchyma, and tested this hypothesis by developing and evaluating a self-healing hydrogel that mimicked both the composition and viscoelasticity of native brain parenchyma. The hydrogel was crosslinked by dynamic boronate ester bonds between phenylboronic acid grafted hyaluronic acid (HA-PBA) and dopamine grafted gelatin (Gel-Dopa). This HA-PBA/Gel-Dopa hydrogel could be injected into a lesion cavity in a shear-thinning manner with rapid hemostasis, high tissue adhesion and efficient self-healing. We tested this in an in vivo mouse model of brain lesions and found the hydrogel to support neural cell infiltration, decrease astrogliosis and glial scars, and close the lesions. The results suggest a role for viscoelasticity in brain lesion healing, and motivate additional experimentation in larger animals as the technology progresses towards potential application in humans.
Mechanical forces impair antigen discrimination by reducing differences in T cell receptor off-rates
Authors: Pettmann Johannes , Awada Lama , Różycki Bartosz , Huhn Anna , Faour Sara , Kutuzov Mikhail , Limozin Laurent , Weikl Thomas R. , van der Merwe P. Anton , Robert Philippe , Dushek Omer
Published: May 2022

T cells use their T cell receptors (TCRs) to discriminate between lower-affinity self and higher-affinity foreign peptide major-histocompatibility-complexes (pMHCs) based on the TCR/pMHC off-rate. It is now appreciated that T cells generate mechanical forces during this process but how force impacts the TCR/pMHC off-rate remains unclear. Here, we measured the effect of mechanical force on the off-rate of multiple TCR/pMHC interactions. Unexpectedly, we found that lower-affinity pMHCs with faster solution off-rates were more resistant to mechanical force (weak slip or catch bonds) than higher-affinity interactions (strong slip bonds), and this was confirmed by molecular dynamic simulations. Consistent with these findings, we show that the best characterized catch-bond, involving the OT-I TCR, has a low affinity and an exceptionally fast solution off-rate. Our findings imply that reducing forces on the TCR/pMHC interaction improves antigen discrimination and we suggest this new force-shielding role for the adhesion receptors CD2 and LFA-1.

One sentence summary

Mechanical forces disproportionately accelerate the off-rates of higher-affinity antigens reducing T cell antigen discrimination
SOPHIE: viral outbreak investigation and transmission history reconstruction in a joint phylogenetic and network theory framework
Authors: Skums Pavel , Mohebbi Fatemeh , Tsyvina Vyacheslav , Baykal Pelin Icer , Nemira Alina , Ramachandran Sumathi , Khudyakov Yury
Published: May 2022

Genomic epidemiology is now widely used for viral outbreak investigations. Still, this methodology faces many challenges. First, few methods account for intra-host viral diversity. Second, maximum parsimony principle continues to be employed, even though maximum likelihood or Bayesian models are usually more consistent. Third, many methods utilize case-specific data, such as sampling times or infection exposure intervals. This impedes study of persistent infections in vulnerable groups, where such information has a limited use. Finally, most methods implicitly assume that transmission events are independent, while common source outbreaks violate this assumption.

We propose a maximum likelihood framework SOPHIE (SOcial and PHilogenetic Investigation of Epidemics) based on integration of phylogenetic and random graph models. It infers transmission networks from viral phylogenies and expected properties of inter-host social networks modelled as random graphs with given expected degree distributions. SOPHIE is scalable, accounts for intra-host diversity and accurately infers transmissions without case-specific epidemiological data. SOPHIE code is freely available at https://github.com/compbel/SOPHIE/
Association of variants in ACE, ACTN3, AGT, IL6 and BDKRB2 genes with athlete status and playing position in Colombian amateur rugby athletes
Authors: Paz Garcia Efraín , Gonzalez Gerardo David , Barreto Guillermo
Published: May 2022

Genetic polymorphisms are involved in different metabolic pathways that are manifested at the physiological level and have been associated with specific phenotypes in sport from anthropometric and functional characterizations that pose conditional and physiological demands for the rugby athlete. The identification of this type of polymorphisms in athletes represents a resource that contributes significantly to the processes of training, selection and sports orientation.

The purpose of this study was to describe type and frequencies of allelic and genotypic variants in ACTN3, ACE, AGT, BDRKB2 and IL6 genes in sub elite rugby athletes in Colombia. Additionally, the polymorphisms found were compared with a control population, as well as contrasted according to playing position backs and forwards.

In this research, 47 individuals from the Vallecaucana rugby league and 67 from a control group (non-athletes) were sampled. All were analyzed for polymorphisms in the ACE, AGT, ACTN3, IL6 and BDKRB2 genes, using the PCR RFLPs technique. The significance of the differences between the experimental and control groups was tested by the X2 test (p <0.05).

In rugby athletes we found a higher frequency of allele D (0.883) ACE gene, allele R (0.63) ACTN3 gene, allele G (0.819) IL6 gene, all associated with strength and power sports. There are significant genotypic differences between athletes and the control population in all the genes analyzed and significant allelic differences in the ACE, ACTN3, BDRKB2 and IL6 genes. When comparing the playing positions (backs vs. forwards), significant genotypic differences were observed in the ACTN3, BDRKB2, AGT and IL6 genes. At the allelic level, the R and X alleles of the ACTN3 gene and the I allele of the ACE gene show significant differences.

In conclusion, in the polymorphisms analyzed, an association with strength sports, explosive strength and rugby is observed. Significant genotypic and allelic differences were also recorded between the backs and forwards positions, as well as significant differences in the allelic and genotypic structure between the group of athletes and the control population.
Maintenance of neurotransmitter identity by Hox proteins through a homeostatic mechanism
Authors: Feng Weidong , Destain Honorine , Smith Jayson J , Kratsios Paschalis
Published: May 2022

Hox transcription factors play fundamental roles during early patterning, but they are also expressed continuously – from embryo through adulthood – in the nervous system. The functional significance of their sustained expression remains unclear. In C. elegans motor neurons (MNs), we find that LIN-39 (Scr/Dfd/Hox4-5) is continuously required during post-embryonic life to maintain neurotransmitter identity, a core element of neuronal function. LIN-39 acts directly to co-regulate genes that define cholinergic identity (e.g., unc-17/VAChT, cho-1/ChT). We further show that LIN-39, MAB-5 (Antp/Hox6-8) and the transcription factor UNC-3 (Collier/Ebf) operate in a positive feedforward loop to ensure continuous and robust expression of cholinergic identity genes. Finally, we identify a two-component, design principle (Hox transcriptional autoregulation counterbalanced by negative UNC-3 feedback) for homeostatic control of Hox gene expression in adult MNs. These findings uncover a noncanonical role for Hox proteins during post-embryonic life, critically broadening their functional repertoire from early patterning to the control of neurotransmitter identity.
A new, Critically Endangered species of Impatiens (Balsaminaceae) from the coastal plain of the Republic of Congo
Authors: Cheek Martin
Published: May 2022

Impatiens moutsambotei is described from a herbarium specimen collected at a waterfall in forest on the coastal plain, below the Mayombe Mts of the Republic of Congo. Sharing many distinctive characters with Impatiens floretii of the Doudou Mts of Gabon, it is abundantly distinguished inter alia by the leaf-blades which are lanceolate or narrowly elliptic, not ovate, their bases acute, not obtuse or broadly rounded to truncate; the reduced, peduncular bracts bearing long, filiform setae, and not entire; the proximal (upper) of the lateral united petals are entire, not bifid; the spur is curved at the base and overlaps the lower sepal, not curved through its length to describe a semi-circle and held below the lower sepal. Both species are placed in the Impatiens macroptera species aggregate. Impatiens moutsambotei is known from a single site, where it was collected nearly 30 years ago and not seen since. The new species is assessed as Critically Endangered due to threats of habitat clearance from mining and road widening, and may be already be extinct.
Multicomponent Pseudomonas aeruginosa vaccines eliciting Th17 cells and functional antibody responses confer enhanced protection against experimental acute pneumonia in mice
Authors: Shaikh Mohammad Omar Faruk , Schaefers Matthew M. , Merakou Christina , DiBlasi Marco , Bonney Sarah , Liao Tiffany , Zurakowski David , Kehl Margaret , Tabor David E. , DiGiandomenico Antonio , Priebe Gregory P.
Published: May 2022

The Gram-negative pathogen Pseudomonas aeruginosa is a common cause of pneumonia in hospitalized patients. Its increasing antibiotic resistance and widespread occurrence present a pressing need for vaccines. We previously showed that a P. aeruginosa type III secretion system protein, PopB elicits a strong Th17 response in mice after intranasal (IN) immunization and confers antibody-independent protection against pneumonia in mice. In the current study, we evaluated the immunogenicity and protective efficacy in mice of the combination of PopB (purified with its chaperone protein PcrH) and OprF/I, an outer membrane hybrid fusion protein, compared to immunization with the proteins individually either by the intranasal (IN) or subcutaneous (SC) routes. Our results show that after vaccination, a Th17 recall response from splenocytes was detected only in mice vaccinated with PopB/PcrH, either alone or in combination with OprF/I. Mice that were immunized with the combination of PopB/PcrH and OprF/I had enhanced protection in an acute lethal P. aeruginosa pneumonia model, regardless of vaccine route, compared to the mice vaccinated the with either alone or adjuvant control. Immunization generated IgG titers against the vaccine proteins and whole P. aeruginosa cells. Interestingly, none of these antisera had opsonophagocytic killing activity, but antisera from mice immunized with vaccines containing OprF/I had the ability to block IFN-γ binding to OprF/I, a known virulence mechanism. Hence, vaccines combining PopB/PcrH with OprF/I that elicit functional antibodies lead to a broadly and potently protective vaccine against P. aeruginosa pulmonary infections.
Spermine inhibits pathogen-associated molecular pattern (PAMP) ROS and Ca2+ burst and reshapes the transcriptional landscape of PAMP-triggered immunity in Arabidopsis thaliana
Authors: Zhang Chi , Atanasov Kostadin E. , Alcázar Rubén
Published: May 2022

Polyamines are small polycationic amines which levels increase during defense. Previous studies support the contribution of the polyamine spermine (Spm) to the establishment of the hypersensitive response (HR) during incompatible plant-pathogen interactions. However, the potential contribution of Spm to other layers of defense, and pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI) in particular, was not completely established. Here we compared the contribution of Spm and putrescine (Put) to early and late PTI responses. We find that Put and Spm show opposite effects on PAMP-elicited reactive oxygen species (ROS) production, with Put increasing whereas Spm lowering flg22-stimulated ROS burst. Through genetic and pharmacological approaches, we find that the inhibitory effect of Spm on flg22-elicited ROS is independent of polyamine oxidation and EDS1 (ENHANCED DISEASE SUSCEPTIBILITY 1), PAD4 (PHYTOALEXIN DEFICIENT 4), salicylic acid and NPR1 (NONEXPRESSER OF PR GENES 1) defense components but resembles chemical inhibition of RBOHD (RESPIRATORY BURST OXIDASE HOMOLOG D) function. Remarkably, Spm can also suppress ROS elicited by FLS2-independent but RBOHD-dependent pathways, thus pointing to compromised RBOHD function. Consistent with this, we find that Spm dampens flg22-stimulated cytosolic Ca2+ influx necessary for RBOHD function and reshapes the transcriptional landscape of PTI and defense responses against Pseudomonas syringae pv. tomato DC3000. Overall, we provide molecular evidence for the differential contribution of Put and Spm to PTI with an impact on plant defense.
Feature-space selection with banded ridge regression
Authors: la Tour Tom Dupré , Eickenberg Michael , Nunez-Elizalde Anwar O. , Gallant Jack L.
Published: May 2022

Encoding models provide a powerful framework to identify the information represented in brain recordings. In this framework, a stimulus representation is expressed within a feature space and is used in a regularized linear regression to predict brain activity. To account for a potential complementarity of different feature spaces, a joint model is fit on multiple feature spaces simultaneously. To adapt regularization strength to each feature space, ridge regression is extended to banded ridge regression, which optimizes a different regularization hyperparameter per feature space. The present paper proposes a method to decompose over feature spaces the variance explained by a banded ridge regression model. It also describes how banded ridge regression performs a feature-space selection, effectively ignoring non-predictive and redundant feature spaces. This feature-space selection leads to better prediction accuracy and to better interpretability. Banded ridge regression is then mathematically linked to a number of other regression methods with similar feature-space selection mechanisms. Finally, several methods are proposed to address the computational challenge of fitting banded ridge regressions on large numbers of voxels and feature spaces. All implementations are released in an open-source Python package called Himalaya.
SWEET13 transport of sucrose, but not gibberellin, restores male fertility in Arabidopsis sweet13;14
Authors: Isoda Reika , Palmai Zoltan , Yoshinari Akira , Chen Li Qing , Tama Florence , Frommer Wolf B. , Nakamura Masayoshi
Published: May 2022

SWEET sucrose transporters play important roles in the allocation of sucrose in plants. Some SWEETs were shown to also mediate transport of the plant growth regulator gibberellin (GA). The close physiological relationship between sucrose and GA raised the questions of if there is a functional connection, and whether one or both of the substrates are physiologically relevant. To dissect these two activities, molecular dynamics were used to map the binding sites of sucrose and GA in the pore of SWEET13 and predicted binding interactions that might be selective for sucrose or GA. Transport assays confirmed these predictions. In transport assays, the N76Q mutant had 7x higher relative GA3 activity, and the S142N mutant only transported sucrose. The impaired pollen viability and germination in sweet13;14 double mutants were complemented by the sucrose-selective SWEET13S142N but not by the SWEET13N76Q mutant, indicating that sucrose is the physiologically relevant substrate and that GA transport capacity is dispensable in the context of male fertility. Therefore, GA supplementation to counter male sterility may act indirectly via stimulating sucrose supply in male sterile mutants. These findings are also relevant in the context of the role of SWEETs in pathogen susceptibility.
NaV1.1 is essential for proprioceptive signaling and motor behaviors
Authors: Espino Cyrrus M. , Lewis Cheyanne M. , Ortiz Serena , Dalal Miloni S. , Garlapalli Snigdha , Wells Kaylee M. , O’Neil Darik A. , Wilkinson Katherine A. , Griffith Theanne N.
Published: May 2022

Abstract

The voltage-gated sodium channel (NaV), NaV1.1, is well-studied in the central nervous system; conversely, its contribution to peripheral sensory neuron function is more enigmatic. Here, we identify a new role for NaV1.1 in mammalian proprioception. RNAscope analysis and in vitro patch clamp recordings in genetically identified mouse proprioceptors show ubiquitously channel expression and significant contributions to intrinsic excitability. Notably, genetic deletion of NaV1.1 in sensory neurons caused profound and visible motor coordination deficits in conditional knockout mice of both sexes, similar to conditional Piezo2-knockout animals, suggesting this channel is a major contributor to sensory proprioceptive transmission. Ex vivo muscle afferent recordings conditional knockout mice found that loss of NaV1.1 leads to inconsistent and unreliable proprioceptor firing characterized by action potential failures during static muscle stretch; conversely, afferent responses to dynamic vibrations were unaffected. This suggests that while a combination of Piezo2 and other NaV isoforms are sufficient to elicit activity in response to transient stimuli, NaV1.1 is required for transmission of receptor potentials generated during sustained muscle stretch. Impressively, recordings from afferents of heterozygous conditional knockout animals were similarly impaired, and heterozygous conditional knockout mice also exhibited motor behavioral deficits. Thus, NaV1.1 haploinsufficiency in sensory neurons impairs both proprioceptor function and motor behaviors. Importantly, human patients harboring NaV1.1 loss-of-function mutations often present with motor delays and ataxia; therefore, our data suggest sensory neuron dysfunction contributes to the clinical manifestations of neurological disorders in which NaV1.1 function is compromised. Collectively, we present the first evidence that NaV1.1 is essential for mammalian proprioceptive signaling and behaviors.
Serine Deamination as a New Acid Resistance Mechanism in Escherichia coli
Authors: Wiebe Michelle A. , Brannon John R. , Steiner Bradley D. , Bamidele Adebisi , Schrimpe-Rutledge Alexandra C. , Codreanu Simona G. , Sherrod Stacy D. , McLean John A. , Hadjifrangiskou Maria
Published: May 2022

Escherichia coli associates with humans early in life and can occupy several body niches either as a commensal in the gut and vagina, or as a pathogen in the urinary tract. As such, E. coli has an arsenal of acid response mechanisms that allow it to withstand the different levels of acid stress encountered within and outside the host. Here, we report the discovery of an additional acid response mechanism that involves the deamination of L-serine to pyruvate by the conserved L-serine deaminases SdaA and SdaB. L-serine is the first amino acid to be imported in E. coli during growth in laboratory media, as the culture senesces. However, there remains a lack in knowledge as to why L-serine is preferred and how it is utilized. We show that in acidified media, L-serine is brought into the cell via the SdaC transporter and deletion of both SdaA and SdaB renders E. coli susceptible to acid stress, with a phenotype similar to other acid stress deletion mutants. We also show that the pyruvate produced by L-serine de-amination activates the pyruvate sensor BtsS, which in concert with the non-cognate response regulator YpdB upregulates the putative transporter YhjX, similar to what has been reported for this system during transition of E. coli to stationary phase. Based on these observations, we propose that L-serine deamination constitutes another acid response mechanism in E. coli that may function to protect E. coli as it transitions to stationary phase of growth.

IMPORTANCE

The observation that L-serine uptake occurs as an E. coli culture senesces is well-established, yet the benefit E. coli garners from this uptake remains unclear. Here, we report a novel acid resistance mechanism, where L-serine is deaminated to pyruvate and ammonia, promoting acid tolerance in E. coli. This study is important as it provides evidence of the use of L-serine as an acid response strategy, not previously reported for E. coli.
Intracellular connections between basal bodies promote the coordinated behavior of motile cilia
Authors: Soh Adam W. J. , Woodhams Louis G. , Junker Anthony D. , Enloe Cassidy M. , Noren Benjamin E. , Harned Adam , Westlake Christopher J. , Narayan Kedar , Oakey John S. , Bayly Philip V. , Pearson Chad G.
Published: May 2022

Hydrodynamic flow produced by multi-ciliated cells is critical for fluid circulation and cell motility. Hundreds of cilia beat with metachronal synchrony for fluid flow. Cilia-driven fluid flow produces extracellular hydrodynamic forces that cause neighboring cilia to beat in a synchronized manner. However, hydrodynamic coupling between neighboring cilia is not the sole mechanism that drives cilia synchrony. Cilia are nucleated by basal bodies (BBs) that link to each other and to the cell’s cortex via BB-associated appendages. The intracellular BB and cortical network is hypothesized to synchronize ciliary beating by transmitting cilia coordination cues. The extent of intracellular ciliary connections and the nature of these stimuli remain unclear. Moreover, how BB connections influence the dynamics of individual cilia has not been established. We show by FIB-SEM imaging that cilia are coupled both longitudinally and laterally in the ciliateTetrahymena thermophilaby the underlying BB and cortical cytoskeletal network. To visualize the behavior of individual cilia in live, immobilizedTetrahymenacells, we developedDelivered IronParticleUbietyLiveLight-(DIPULL) microscopy. Quantitative and computer analyses of ciliary dynamics reveal that BB connections control ciliary waveform and coordinate ciliary beating. Loss of BB connections reduces cilia-dependent fluid flow forces.

Soh et al investigate whether intracellular connections between basal bodies control ciliary behavior in multi-ciliated cells. Using aTetrahymenalive cell immobilization technique to quantify ciliary dynamics, they show that inter-BB connections are required for effective ciliary waveform and coordinated ciliary beating that promotes fluid flow.
Fluorescence fluctuation based super resolution microscopy, basic concepts for an easy start
Authors: Alva Alma , Brito-Alarcón Eduardo , Linares Alejandro , Torres-García Esley , O. Hernández Haydeé , Pinto-Cámara Raúl , Martínez Damián , Hernández-Herrera Paul , D’Antuono Rocco , Wood Christopher , Guerrero Adán
Published: May 2022

Due to the wave nature of light, optical microscopy has a lower-bound lateral resolution limit of about half of the wavelength of the detected light, i.e., within the range of 200 to 300 nm. The Fluorescence Fluctuation based Super Resolution Microscopy (FF-SRM) encompases a collection of image analysis techniques which rely on the statistical processing of temporal variations of fluorescence to reduce the uncertainty about the fluorophore positions within a sample, hence, bringing spatial resolution down to several tens of nm. The FF-SRM is known to be suitable for live-cell imaging due to its compatibility with most fluorescent probes and lower instrumental and experimental requirements, which are mostly camera-based epifluorescence instruments. Each FF-SRM approach has strengths and weaknesses, which depend directly on the underlying statistical principles through which enhanced spatial resolution is achieved. In this review, the basic concepts and principles behind a range of FF-SRM methods published to date are revisited. Their operational parameters are explained and guidance for its selection is provided.
Density-Dependent Color Scanning Electron Microscopy (DDC-SEM) for calcified tissue and pathological calcification
Authors: Tsolaki Elena , Chester Adrian H , Bertazzo Sergio
Published: May 2022

Scanning electron microscopy (SEM) is widely used for materials characterization. It has also been successfully applied to the imaging of biological samples, providing invaluable insights into the topography, morphology and composition of biological structures, including pathological minerals, in diseases affecting cardiovascular, kidney and ocular tissues. Here we provide a comprehensive and detailed guide on how to use colored SEM to aid the visualization and characterization of pathological calcification, and identify the effects of different sample preparation protocols for the visualisation of these minerals.
ReCSAI: Recursive compressed sensing artificial intelligence for confocal lifetime localization microscopy
Authors: Reinhard Sebastian , Helmerich Dominic A. , Boras Dominik , Sauer Markus , Kollmannsberger Philip
Published: May 2022

Localization-based super-resolution microscopy resolves macromolecular structures down to a few nanometers by computationally reconstructing fluorescent emitter coordinates from diffraction-limited spots. The most commonly used algorithms are based on fitting parametric models of the point spread function (PSF) to a measured photon distribution. These algorithms make assumptions about the symmetry of the PSF and thus, do not work well with irregular, non-linear PSFs that occur for example in confocal lifetime imaging, where a laser is scanned across the sample. An alternative method for reconstructing sparse emitter sets from noisy, diffraction-limited images is compressed sensing, but due to its high computational cost it has not yet been widely adopted. Deep neural network fitters have recently emerged as a new competitive method for localization microscopy. They can learn to fit arbitrary PSFs, but require extensive simulated training data and do not generalize well. A method to efficiently fit the irregular PSFs from confocal lifetime localization microscopy combining the advantages of deep learning and compressed sensing would greatly improve the acquisition speed and throughput of this method. Here we introduce ReCSAI, a compressed sensing neural network to reconstruct localizations for confocal dSTORM, together with a simulation tool to generate training data. We implemented and compared different artificial network architectures, aiming to combine the advantages of compressed sensing and deep learning. We found that a U-Net with a recursive structure inspired by iterative compressed sensing showed the best results on realistic simulated datasets with noise, as well as on real experimentally measured confocal lifetime scanning data. Adding a trainable wavelet denoising layer as prior step further improved the reconstruction quality. Our deep learning approach can reach a similar reconstruction accuracy for confocal dSTORM as frame binning with traditional fitting without requiring the acquisiton of multiple frames. In addition, our work offers generic insights on the reconstruction of sparse measurements from noisy experimental data by combining compressed sensing and deep learning. We provide the trained networks, the code for network training and inference as well as the simulation tool as python code and Jupyter notebooks for easy reproducibility.
Conserved population dynamics in the cerebro-cerebellar system between waking and sleep
Authors: Xu Wei , De Carvalho Felipe , Jackson Andrew
Published: May 2022

Despite the importance of the cerebellum for motor learning, and the recognised role of sleep in motor memory consolidation, surprisingly little is known about activity in the sleeping cerebro-cerebellar system. Here we used wireless recording from M1 and the cerebellum in monkeys to examine the relationship between patterns of single-unit spiking activity observed during waking behaviour and in natural sleep. Across the population of recorded units, we observed similarities in the timing of firing relative to local field potential features associated with both movements during waking and up-states during sleep. We also observed a consistent pattern of asymmetry in pair-wise cross-correlograms, indicative of preserved sequential firing in both wake and sleep at low frequencies. Despite the overall similarity in population dynamics between wake and sleep, there was a global change in the timing of cerebellar activity relative to motor cortex, from contemporaneous in the awake state, to motor cortex preceding the cerebellum in sleep. We speculate that similar population dynamics in waking and sleep may imply that cerebellar internal models are activated in both states, but that their output is decoupled from motor cortex in sleep. Nevertheless, spindle frequency coherence between the cerebellum and motor cortex may provide a mechanism for cerebellar computations to influence sleep-dependent learning processes in the cortex.

Significance statement

It is well known that sleep can lead to improved motor performance. One possibility is that synaptic changes during sleep result from off-line repetitions of neuronal activity patterns in brain areas responsible for the control of movement. In this study we show for the first time that neuronal patterns in the cerebro-cerebellar system are conserved during both movements and sleep up-states, albeit with a shift in the relative timing between areas. Additionally, we show the presence of simultaneous M1-cerebellar spike coherence at spindle frequencies associated with up-state replay and postulate that this is a mechanism whereby a cerebellar internal models can shape plasticity in neocortical circuits during sleep.
Heart Rate Variability Covaries with Amygdala Functional Connectivity During Voluntary Emotion Regulation
Authors: Tupitsa Emma , Egbuniwe Ifeoma , Lloyd William K. , Puertollano Marta , Macdonald Birthe , Joanknecht Karin , Sakaki Michiko , van Reekum Carien M.
Published: May 2022

The Neurovisceral Integration Model posits that shared neural networks support the effective regulation of emotions and heart rate, with heart rate variability (HRV) serving as an objective, peripheral index of prefrontal inhibitory control. Prior neuroimaging studies have predominantly examined both HRV and associated neural functional connectivity at rest, as opposed to contexts that require active emotion regulation. The present study sought to extend upon previous resting-state functional connectivity findings, examining HRV and corresponding amygdala functional connectivity during a cognitive reappraisal task. Seventy adults (52 old and 18 young adults, 18-84 years, 51% male) received instructions to cognitively reappraise negative and neutral affective images during functional MRI scanning. HRV measures were derived from a finger pulse signal throughout the scan. During the task, young adults exhibited a significant inverse association between HRV and amygdala-medial prefrontal cortex (mPFC) functional connectivity, in which higher HRV was correlated with weaker amygdala-mPFC coupling, whereas old adults displayed a slight positive, albeit non-significant correlation. Furthermore, voxelwise whole-brain functional connectivity analyses showed that higher HRV was linked to weaker right amygdala-posterior cingulate cortex connectivity across old and young adults, and in old adults, higher HRV positively correlated with stronger right amygdala – right ventrolateral prefrontal cortex connectivity. Collectively, these findings highlight the importance of assessing HRV and neural functional connectivity during active regulatory contexts to further identify neural concomitants of HRV and adaptive emotion regulation.
Reaction Conditions Promoting the Specific Detection of SARS-CoV-2 NendoU Enzymatic Activity
Authors: Makharashvili Nodar , McNamara James O.
Published: May 2022

Methods that enable rapid detection of SARS-CoV-2 provide valuable tools for detecting and controlling Covid-19 outbreaks and also facilitate more effective treatment of infected individuals. The predominant approaches developed use PCR to detect viral nucleic acids or immunoassays to detect viral proteins. Each approach has distinct advantages and disadvantages, but alternatives that do not share the same limitations could enable substantial improvements in outbreak detection and management. For instance, methods that have comparable sensitivity to PCR, but that are not prone to the false-positive results that stem from the tendency of PCR to detect molecular degradation products could improve accurate identification of infected individuals. An alternative approach with potential to achieve this entails harnessing the unique enzymatic properties of SARS-CoV-2 enzymes to generate SARS-Cov-2-specific signals that indicate the presence of the virus. This route benefits from the high sensitivity provided by enzymatic signal amplification and also the fact that signal is generated only by intact viral enzymes, not degradation products. Here, we demonstrate enzymatic reaction conditions that enable the preferential detection of NendoU of SARS-CoV-2, versus several of its orthologues, with a fluorogenic oligonucleotide substrate. These compositions provide a possible technical foundation for a novel approach for detecting SARS-CoV-2 that has distinct advantages from current approaches.
Allocation of visuospatial attention indexes evidence accumulation for reach decisions
Authors: Schonard Carolin , Heed Tobias , Seegelke Christian
Published: May 2022

Visuospatial attention is a prerequisite for the performance of visually guided movements: Perceptual discrimination is regularly enhanced at target locations prior to movement initiation. It is known that this attentional prioritization evolves over the time of movement preparation; however, it is not clear whether this build-up simply reflects a time requirement of attention formation or whether, instead, attention build-up reflects the emergence of the movement decision. To address this question, we combined behavioral experiments, psychophysics, and computational decision-making models to characterize the time course of attention build-up during motor preparation. Participants (n = 46, 29 female) executed center-out reaches to one of two potential target locations and reported the identity of a visual discrimination target that occurred concurrently at one of various time-points during movement preparation and execution. Visual discrimination increased simultaneously at the two potential target locations but was modulated by the experiment-wide probability that a given location would become the final goal. Attention increased further for the location that was then designated as the final goal location, with a time course closely related to movement initiation. A sequential sampling model of decision-making predicted key temporal characteristics of attentional allocation. Together, these findings provide evidence that visuospatial attentional prioritization during motor preparation does not simply reflect that a spatial location has been selected as movement goal, but rather indexes the time-extended, cumulative decision that leads to selection, hence constituting a link between perceptual and motor aspects of sensorimotor decisions.

Significance statement

When humans perform a goal-directed movement such as a reach, attention shifts towards the goal location already before movement initiation, indicating that motor goal selection relies on the use of attention. Here, we demonstrate that key temporal aspects of visuospatial attention are predicted by a well-known computational model of decision-making. These findings suggest that visual attention signals much more than simply that a motor goal has been selected: instead, the time-course of emergent, visuospatial attention reflects the time-extended, cumulative decision that leads to goal selection, offering a window onto the tight link of perceptual and motor aspects in sensorimotor decision-making.
Depth and evenness of sequence coverage are associated with assembly quality, genome structure, and choice of sequencing platform in archived plastid genomes
Authors: Jenke Nils , Gruenstaeudl Michael
Published: May 2022

In plastid genomes, the depth and evenness of sequence coverage are considered important indicators for assembly quality. However, the precise manifestations that sequencing depth and evenness can have in the assembly of these genomes, as well as any differences across individual genome sections, have yet to be evaluated. This investigation aims to identify the impact that sequencing depth and evenness can have on the assembly of plastid genomes and how both metrics are related to plastid genome structure. Specifically, we assess if sequencing evenness and reduced sequencing depth have significant correlations with, or significant differences among, individual genome sections, assembly quality metrics, the sequencing platforms employed, and the software tools used for genome assembly. To that end, we retrieve published plastid genomes as well as their sequence reads and genome metadata from public databases, measure sequencing depth and evenness across their sequences, and test several hypotheses on genome assembly and structure through non-parametric statistical tests. The results of our analyses show significant differences in sequencing depth across the four structural partitions as well as between the coding and non-coding sections of the plastid genomes, a significant correlation between sequencing evenness and the number of ambiguous nucleotides per genome, and significant differences in sequencing evenness between various sequencing platforms. Based on these results, we conclude that the observed differences and correlations are not a product of chance alone but possibly genuine manifestations of sequencing depth and evenness during the assembly of these genomes.
The impact of network sharing on competition: the challenges posed by 5G
Authors: Pápai Zoltán , McLean Aliz , Nagy Péter , Szabó Gábor , Csorba Gergely
Published: May 2022

Purpose

The paper aims to discuss the expected changes 5G will bring to the assessment of active mobile network sharing agreements from a competition policy point of view.

Design/methodology/approach

The paper distinguishes between current, early 5G networks and the fully-fledged 5G envisioned for the future, then focuses on the main competition concerns where 5G may bring the most significant changes in the evaluation compared to 4G.

Findings

The authors find that while network sharing for early 5G can be evaluated in a similar way to previous generations, fully-fledged 5G can raise new issues. The authors predict these main concerns to be service differentiation, cost commonality between the parties and the parties’ ability and incentives to grant access to critical inputs to downstream competitors. Due to the huge costs of 5G rollout, network sharing is set to become even more widespread than before. For each of the concerns, the authors show that they are not easy to substantiate and they may even become less serious than under 4G.

Originality/value

To the best of the authors’ knowledge, this paper is one of the first contributions to analyse the impact of fully-fledged 5G on mobile network sharing agreements’ competitive assessment.
The spatial pattern and dynamic evolution of basic public service level in Beijing-Tianjin-Hebei region from the perspective of COVID-19
Authors: Wang Lida , Rong Xian , Mu Lingling
Published: May 2022

Purpose

This study aims to investigate the basic public service level in the Beijing-Tianjin-Hebei region under the impact of COVID-19.

Design/methodology/approach

This study constructed a basic public service-level evaluation system from the five dimensions of education, culture, health, social security and infrastructure and environment, and measures the basic public service level in 13 cities in Beijing, Tianjin and Hebei using the entropy method. The spatial pattern and dynamic evolution of the public service level are analysed from the perspective of dynamic trends in time series and spatial distribution, along with the reasons for the evolution of spatial distribution.

Findings

(1) The basic public service level in the 13 cities is generally on the rise, but the trend is unstable. (2) The basic public service level in space shows a general trend of attenuation from northeast to southwest, with significant spatial imbalance and orientation. (3) The regional differences first increase and then decrease. (4) The inter-group mobility of different basic public service levels is low, and cities with lower initial levels find it difficult to achieve leapfrog development. Moreover, the health service level of the region is still at a low stage, which is not conducive to effectively preventing and controlling the epidemic.

Originality/value

From the perspective of this research, the spatial pattern and dynamic evolution of basic public service were adopted to analyse the coordinated development of the Beijing-Tianjin-Hebei region. Furthermore, this study discusses how to improve the basic public service level to ensure sustainable operation in the region under the impact of COVID-19.
Collective turnover and unit performance: moderation effects of work experience and time clustering of quits
Authors: Simón Cristina , Shaw Jason D. , de Sivatte Isabel , Olmos Albacete Ricardo
Published: May 2022

Purpose

The authors propose and test these boundary conditions to the relationship between voluntary collective turnover and unit performance: job and organizational tenure and the time clustering of turnover.

Design/methodology/approach

The authors analyze longitudinal data obtained from 231 units of an international clothing retailer in Spain assessed during 36 months.

Findings

The authors show that when the remaining workforce has moderate, but not low or high, levels of job and organizational tenure, the negative effect of quits on performance is buffered. Furthermore, their results show that time-clustered voluntary turnover patterns have stronger negative effects on unit performance than turnover patterns spread over time.

Originality/value

The authors extend the collective turnover literature addressing two qualitative properties of the content of voluntary turnover, the experience of the workers that remain in the unit after the turnover events happen and how these events are clustered/dispersed over time.
The path from social and organizational resources to satisfaction: the mediating role of academic engagement and the moderating role of psychological capital
Authors: Junça Silva Ana , Abreu Pedro , Brito Sílvio
Published: May 2022

Purpose

This study draws on the Job Demands-Resources (JD-R) model to analyze if (1) social and organizational resources impact students' satisfaction, via academic engagement, and (2) psychological capital moderates the mediating path.

Design/methodology/approach

To test our hypotheses, the authors collected data from two well-established higher education institutions (HEIs), in which 840 students participated.

Findings

Additionally, the results demonstrated that the indirect relationship between resources and satisfaction through academic engagement was conditional on the individual's levels of psychological capital, in such a way that it became stronger for those who presented lower levels of psychological capital, compared to those with higher levels. The students' satisfaction can be an indicator of the institution's perceived quality, in addition to positioning the HEI as a healthy organization.

Research limitations/implications

The cross-sectional design of the study is a limitation.

Practical implications

The students' satisfaction levels can be an indicators of the institution's perceived quality, in addition to positioning the HEI as a healthy organization. Thus, these conclusions can contribute to guiding the actors of HEIs in designing and promoting interventions to promote students' satisfaction.

Originality/value

However, the study presents some guidelines for academic and organizational practice, namely regarding the relevance of resources for increasing academic engagement and, consequently, satisfaction.
The tension between INGOs’ accountability to donors’ agendas and to the affected population and its impact on their access to human rights
Authors: Zibin Tamara , Zibin Aseel , Al-Essa Ayman
Published: May 2022

Purpose

This paper aims to discuss the main reasons behind the tension between accountability to donors and accountability to beneficiaries, in terms of obtaining the basic needs and human rights of the latter. Relying on three arguments; firstly, based on Angela Crack’s (2013) theory of the three waves of accountability, the authors argue that the unequal power relations between donors, international non-governmental organisations (INGOs) and beneficiaries is a source of the deficit and gap of this accountability. Secondly, the authors examine the relation between INGOs and politics, their role in influencing policy making and their increased involvement with governments and states. The authors suggest that INGOs reliance on governments for facilitation and funding makes them accountable to those governments in a way that conflicts with the needs of their beneficiaries affecting their chances to obtain their basic human rights. Thirdly, the authors explore the different agendas between the global north and global south, considering the Western roots of INGOs. Finally, the paper suggests that unequal power relations, INGOs’ questionable legitimacy and the unclear relation with politics explain the causes behind the tension in accountability making it inevitable.

Design/methodology/approach

Angela Crack’s (2013) theory of the three waves of accountability.

Findings

The paper suggests that unequal power relations, INGOs’ questionable legitimacy and the unclear relation with politics explain the causes behind the tension in accountability making it inevitable.

Originality/value

Identifying and resolving the tension between INGOs accountability to donors and accountability to so-called beneficiaries can result in better obtainment of human rights.