bluuebunny/crossref_metadata_2025 huggingface dataset:
Escherichia coliisolated from commercial layer hens in Australia remain susceptible to critically important antimicrobials
Authors: Abraham Rebecca , Allison Hui San , Lee Terence , Pavic Anthony , Chia Raymond , Hewson Kylie , Lee Zheng Z , Hampson David J , Jordan David , Abraham Sam
Published: February 2023

Controlling the use of the most critically important antimicrobials (CIAs) in food animals has been identified as one of the key measures required to curb the transmission of antimicrobial resistant bacteria from animals to humans. Expanding the evidence demonstrating the effectiveness of restricting CIA usage for preventing the emergence of resistance to key drugs amongst commensal organisms in animal production would do much to strengthen international efforts to control antimicrobial resistance (AMR). As Australia has strict controls on antimicrobial use in layer hens, and internationally comparatively low levels of poultry disease due to strict national biosecurity measures, we investigated whether these circumstances have resulted in curtailing development of critical forms of AMR. The work comprised a cross-sectional national survey of 62 commercial layer farms with each assessed for AMR inEscherichia coliisolates recovered from faeces. Minimum inhibitory concentration analysis using a panel of 13 antimicrobials was performed on 296 isolates with those exhibiting phenotypic resistance to fluoroquinolones (a CIA) or multi-class resistance (MCR) subjected to whole genome sequencing. Overall, 52.0% of the isolates were susceptible to all antimicrobials tested, and all isolates were susceptible to ceftiofur, chloramphenicol and colistin. Resistance was observed to ampicillin (16.2%), cefoxitin (1.4%), ciprofloxacin (2.7%), florfenicol (2.4%), gentamicin (1.0%), streptomycin (4.7%), tetracycline (37.8%) and trimethoprim/sulfamethoxazole (10.5%). Multi-class resistance was observed in 23 isolates (7.7%), with one isolate (ST746) exhibiting resistance to five antimicrobial classes. Whole genome sequencing found that ciprofloxacin-resistant (fluoroquinolone) isolates were devoid of both known chromosomal mutations in the quinolone resistance determinant regions and plasmid-mediated quinolone resistance genes (qnr) - other than in one isolate (ST155) which carried theqnrSgene. Two MCRE. coliisolates with ciprofloxacin-resistance were found to be carrying known resistance genes includingaadA1, dfrA1, strA, strB, sul1, sul2, tet(A), blaTEM-1B, qnrS1andtet(A). Overall, this study found thatE. colifrom layer hens in Australia have low rates of AMR, likely due to strict control on antimicrobial usage achieved by the sum of regulation and voluntary measures.
No Evidence in Favour of the Existence of ‘Intentional’ Binding
Authors: Kong Gaiqing , Aberkane Cheryne , Desoche Clément , Farnè Alessandro , Vernet Marine
Published: February 2023

Intentional binding refers to the subjective temporal compression between a voluntary action and its subsequent sensory outcome. Despite some studies challenging the link between temporal compression and intentional action, intentional binding is still widely used as an implicit measure for the sense of agency. The debate remains unsettled primarily because the experimental conditions used in previous studies were confounded with various alternative causes for temporal compression, and action intention has not yet been tested comprehensively against all potential alternative causes in a single study. Here, we solve this puzzle by jointly comparing participants’ estimates of the interval between three types of triggering events with comparable predictability - voluntary movement, passive movement, and external sensory event - and an external sensory outcome (auditory or visual across experiments). The results failed to show intentional binding, i.e., no shorter interval estimation for the voluntary than the passive movement conditions. Instead, we observed temporal (but not intentional) binding when comparing both movement conditions with the external sensory condition. Thus, temporal binding appears to originate from sensory integration and temporal prediction, not from action intention. As such, these findings underscore the need to reconsider the use of “intentional binding” as a reliable proxy of the sense of agency.

Public Significance Statement

When we press a light switch and observe a bulb lightening, we experience a sense of agency, a feeling of control over these events. We often perceive the temporal interval between our voluntary action and its consequence as shorter compared to the same interval between two events we are not involved. Such temporal binding has commonly been taken as a measure of the sense of agency. However, our study reveals that voluntary actions are neither necessary nor sufficient for temporal binding. Instead, temporal binding relies on predicting and integrating information. The sense of agency can be disturbed in various psychiatric disorders, and its brain mechanisms are currently being actively explored. Our study urges amending how it is measured.
The maize preligule band is subdivided into distinct domains with contrasting cellular properties prior to ligule outgrowth
Authors: Neher Wesley , Rasmussen Carolyn G. , Braybrook Siobhan A. , Lažetić Vladimir , Stowers Claire E. , Mooney Paul T. , Sylvester Anne W. , Springer Patricia S.
Published: February 2023

The maize ligule is a fringe of epidermis-derived tissue, which arises from the preligule band (PLB) at a boundary between the blade and sheath. A hinge-like auricle also develops immediately distal to the ligule and contributes to blade angle. Here, we characterize the stages of PLB and early ligule development in terms of topography, cell area, division orientation, cell wall rigidity, and auxin response dynamics. Differential thickening of epidermal cells and localized periclinal divisions contributed to the formation of a ridge within the PLB, which ultimately produces the ligule fringe. Patterns in cell wall rigidity were consistent with the subdivision of the PLB into two regions along a distinct line positioned at the nascent ridge. The proximal region produces the ligule, while the distal region contributes to one epidermal face of the auricles. Whereas the auxin transporter PIN1 accumulated in the PLB, observed differential auxin transcriptional response did not underlie the partitioning of the PLB. Our data demonstrate that two zones with contrasting cellular properties, the preligule and preauricle, are specified within the ligular region prior to ligule outgrowth.

Summary Statement

Changes in cell geometry, division orientation, and cell wall mechanics underlie maize ligule morphogenesis. The establishment of mechanically distinct epidermal domains coincides with topographical changes during early ligule outgrowth.
A Zika virus-responsive sensor-effector system inAedes aegypti
Authors: Basu Sanjay , Reitmayer Christine M. , Lumley Sarah , Atkinson Barry , Schade-Weskott Mathilde L. , Rooney Sara , Larner Will , Montiel Eugenia E. , Gutiérrez-López Rafael , Levitt Emily , Munyanduki Henry M. , Mohamed Ahmed M. E. , Clarke Andrew T. , Koit Sandra , Zusinaite Eva , Fragkoudis Rennos , Merits Andres , Alphey Luke
Published: February 2023

Zika virus (ZIKV) is a recently re-emerged flavivirus transmitted primarily through the bite of an infected mosquito,Aedes aegyptibeing the main vector. ZIKV infection is associated with a range of adverse effects; infection during pregnancy can lead to foetal abnormalities, including microcephaly. Lacking a licensed vaccine, or specific therapeutics, control of ZIKV transmission focuses on vector control. However, in most transmission settings, current methods are insufficient to successfully control ZIKV, or other similarly-transmitted arboviruses such as dengue and chikungunya viruses. This has stimulated interest in genetics-based methods, either to reduce the number of mosquitoes (“population suppression”), or to make mosquitoes less able to transmit (“population modification”). Here, we describe a method to selectively eliminate infected mosquitoes, using a virus sensor inserted into the mosquito genome and coupled to a quorum-counting lethal effector. In mosquitoes, ZIKV normally establishes persistent, lifelong infection; survival of these infected mosquitoes is crucial to transmission potential. Correspondingly, removal of infected mosquitoes can reduce vectorial capacity of a mosquito population, i.e. ability to transmit. Since relatively few mosquitoes become infected, typically <2%, engineered hypersensitivity to ZIKV would have only a modest population-level fitness cost, and lower still if transmission were successfully reduced by such means.
TFEB-vacuolar ATPase signaling regulates lysosomal function and microglial activation in tauopathy
Authors: Wang Baiping , Martini-Stoica Heidi , Qi Chuangye , Lu Tzu-Chiao , Wang Shuo , Xiong Wen , Qi Yanyan , Xu Yin , Sardiello Marco , Li Hongjie , Zheng Hui
Published: February 2023

Transcription factor EB (TFEB) mediates gene expression through binding to theCoordinatedLysosomeExpressionAndRegulation (CLEAR) sequence. TFEB targets include subunits of the vacuolar ATPase (v-ATPase) essential for lysosome acidification. Single nucleus RNA-sequencing (snRNA-seq) of wild-type and PS19 (Tau) transgenic mice identified three unique microglia subclusters in Tau mice that were associated with heightened lysosome and immune pathway genes. To explore the lysosome-immune relationship, we specifically disrupted the TFEB-v-ATPase signaling by creating a knock-in mouse line in which the CLEAR sequence of one of the v-ATPase subunits,Atp6v1h, was mutated. We show that the CLEAR mutant exhibited a muted response to TFEB, resulting in impaired lysosomal acidification and activity. Crossing the CLEAR mutant with Tau mice led to higher tau pathology but diminished microglia response. These microglia were enriched in a subcluster low in mTOR and HIF-1 pathways and was locked in a homeostatic state. Our studies demonstrate a physiological function of TFEB-v-ATPase signaling in maintaining lysosomal homoeostasis and a critical role of the lysosome in mounting a microglia and immune response in tauopathy and Alzheimer’s disease.
Pupil dilation and microsaccades provide complementary insights into the dynamics of arousal and instantaneous attention during effortful listening
Authors: Contadini-Wright Claudia , Magami Kaho , Mehta Nishchay , Chait Maria
Published: February 2023

Listening in noisy environments requires effort – the active engagement of attention and other cognitive abilities, as well as increased arousal. The ability to separately quantify the contribution of these components is key to understanding the dynamics of effort and how it may change across listening situations and in certain populations. We concurrently measured two types of ocular data in young participants (both sexes) - Pupil dilation (PD) (thought to index arousal aspects of effort) and Microsaccades (MS) (hypothesized to reflect automatic visual exploratory sampling) whilst listeners were performing a speech-in-noise task under high- (HL) and low-(LL) perceptual load conditions. Sentences were manipulated so that the behaviourally relevant information (keywords) appeared at the end (Exp1) or beginning (Exp2) of the sentence, resulting in different temporal demands on focused attention. In line with previous reports, PD effects were associated with increased dilation under load. We observed a sustained difference between HL and LL conditions, consistent with increased phasic and tonic arousal. Importantly we show that MS rate was also modulated by perceptual load, manifested as a reduced MS rate in HL relative to LL. Critically, in contrast to the sustained difference seen for PD, MS effects were localised in time, specifically during periods when demands on auditory attention were greatest. These results demonstrate that auditory selective attention interfaces with the mechanisms controlling MS-generation, establishing MS as an informative measure, complementary to PD, with which to quantify the temporal dynamics of auditory attentional processing under effortful listening conditions.

Significance Statement

Listening effort, reflecting the “cognitive bandwidth” deployed to effectively process sound in adverse environments, contributes critically to listening success. Understanding listening effort and the processes involved in its allocation is a major challenge in auditory neuroscience. Here we demonstrate that the microsaccade rate can be used to index a specific sub-component of listening effort - the allocation of instantaneous auditory attention - that is distinct from the modulation of arousal indexed by pupil dilation (currently the dominant measure of listening effot). These results reveal the push-pull process through which auditory attention interfaces with the (visual) attention network that controls microsaccades, establishing microsaccades as a powerful tool for measuring auditory attention and its deficits.
Flexible and cost-effective genomic surveillance ofP. falciparummalaria with targeted nanopore sequencing
Authors: de Cesare Mariateresa , Mwenda Mulenga , Jeffreys Anna E. , Chirwa Jacob , Drakeley Chris , Schneider Kammerle , Ghinai Isaac , Busby George B. , Hamainza Busiku , Hawela Moonga , Bridges Daniel J. , Hendry Jason A.
Published: February 2023

Genomic surveillance ofPlasmodium falciparummalaria can provide policy-relevant information about antimalarial drug resistance, rapid diagnostic test failure, and the evolution of vaccine targets. Yet the large and low complexity genome ofP. falciparumlimits the scope of genomic surveillance, as whole-genome sequencing approaches are costly and targeted approaches are challenging to develop. Moreover, the majority of the morbidity and mortality caused byP. falciparumoccurs in sub-Saharan Africa, where resource constraints can make implementing genomic surveillance difficult. Here, we demonstrate a flexible and cost-effective approach for targeted nanopore sequencing ofP. falciparumto enable genomic surveillance of malaria in low-resource settings. We release open-source software that facilitates rapid and flexible design of amplicon sequencing panels forP. falciparum, coupled with a simple and cost-effective protocol that uses dried blood spots as input. We use this software to design two amplicon panels. The first, called NOMADS8, targets seven major antimalarial drug-resistance associated genes as well as the highly polymorphic genemsp2. The second, NOMAD16, incorporates an additional eight genes including the vaccine targetcspand genes coding for the antigens detected in rapid diagnostic tests,hrp2andhrp3. The panels generate reads between 3 to 4kbp that span the entire coding sequence of most target genes. We validate the panels and protocol on mock and field samples, demonstrating robust sequencing coverage across targets, high single-nucleotide polymorphism calling accuracy within coding sequences, and the ability to explore the within-sample diversity of mixedP. falciparuminfections.
Differential miRNA Expression Contributes to Emergence of Multiple Cancer Stem Cell Subpopulations in Human Colorectal Cancer
Authors: Stark Victoria A. , Facey Caroline O. B. , Opdenaker Lynn , Fields Jeremy Z. , Boman Bruce M.
Published: February 2023

One reason for lack of efficacy in cancer therapeutics is tumor heterogeneity. We hypothesize that tumor heterogeneity arises due to emergence of multiple cancer stem cell (CSC) subpopulations because miRNAs regulate expression of stem cell genes in CSCs. Our goal was to determine if:i) multiple CSC subpopulations exist in a human CRC cell population, andii) miRNAs are differentially expressed in the different CSC subpopulations. We discovered that at least four different CSC populations (ALDH1, CD166, LGR5, LRIG1) exist in the HT29 cell line. CSC subpopulations were quantified using co-staining for multiple stem cell markers, isolated using FACS, and analyzed by NanoString miRNA profiling. The miRNA expression pattern in each CSC subpopulation was analyzed relative to miRNA expression patterns in other CSC subpopulations. Messenger RNAs predicted to be targeted by the upregulated miRNAs in each CSC subpopulation were: 1) identified using bioinformatics analyses, and 2) classified according to their predicted functions using David functional annotation analyses. We found multiple CSC subpopulations with a unique miRNA signature in each CSC subpopulation. Notably, the miRNAs expressed within one CSC subpopulation are predicted to target and downregulate the CSC genes and pathways that establish the other CSC subpopulations. Moreover, mRNAs predicted to be targeted by miRNAs in the different CSC subpopulations have different cellular functional classifications. That different CSC subpopulations express miRNAs that are predicted to target CSC genes expressed in other CSC subpopulations provides a mechanism that might explain the co-existence of multiple CSC subpopulations, tumor heterogeneity, and cancer therapy resistance.
Gaussian Mixture Modeling Extensions for Improved False Discovery Rate Estimation in GC-MS Metabolomics
Authors: Flores Javier E , Bramer Lisa M , Degnan David J , Paurus Vanessa L , Corilo Yuri E , Clendinen Chaevien S
Published: February 2023

The ability to reliably identify small molecules (e.g. metabolites) is key towards driving scientific advancement in metabolomics. Gas chromatography mass spectrometry (GCMS) is an analytic method that may be applied to facilitate this process. The typical GCMS identification workflow involves quantifying the similarity of an observed sample spectrum and other features (e.g. retention index) to that of several references, noting the compound of the best-matching reference spectrum as the identified metabolite. While a deluge of similarity metrics exists, none quantify the error rate of generated identifications, thereby presenting an unknown risk of false identification or discovery. To quantify this unknown risk, we propose a model based framework for estimating the false discovery rate (FDR) among a set of identifications. Extending a traditional mixture modeling framework, our method incorporates both similarity score and experimental information in estimating the FDR. We apply these models to identification lists derived from across 548 samples of varying complexity and sample type (e.g. fungal species, standard mixtures, etc.), comparing their performance to that of the traditional Gaussian mixture model (GMM). Through simulation, we additionally assess the impact of reference library size on the accuracy of FDR estimates. In comparing the best performing model extensions to the GMM, our results indicate relative decreases in median absolute estimation error (MAE) ranging from 12% to 70%, based on comparisons of the median MAEs across all hit lists. Results indicate that these relative performance improvements generally hold despite library size, however FDR estimation error typically worsens as the set of reference compounds diminishes.
Accelerated nanopore basecalling with SLOW5 data format
Authors: Samarakoon Hiruna , Ferguson James M. , Gamaarachchi Hasindu , Deveson Ira W.
Published: February 2023

Nanopore sequencing is emerging as a key pillar in the genomic technology landscape but computational constraints limiting its scalability remain to be overcome. The translation of raw current signal data into DNA or RNA sequence reads, known as ‘basecalling’, is a major friction in any nanopore sequencing workflow. Here, we exploit the advantages of the recently developed signal data format ‘SLOW5’ to streamline and accelerate nanopore basecalling on high-performance computer (HPC) and cloud environments. SLOW5 permits highly efficient sequential data access, eliminating a significant analysis bottleneck. To take advantage of this, we introduceButtery-eel, an open-source wrapper for Oxford Nanopore’sGuppybasecaller that enables SLOW5 data access, resulting in performance improvements that are essential for scalable, affordable basecalling.
No evidence for HPAI H5N1 2.3.4.4b incursion into Australia in 2022
Authors: Wille Michelle , Klaassen Marcel
Published: February 2023

There is an ongoing and profound burden of lineage 2.3.4.4b high pathogenicity avian influenza (HPAI) H5 on wild birds and poultry, globally. Herein we report the continued absence of HPAI in Australia from September – December 2022, in inbound migratory birds. Given the ever changing phenotype of this virus, worldwide studies on the occurence, or here absence of the virus, are of critical importance to understand the virus’ dispersal and incursion risk and development of response strategies.
Changes in physicochemical properties and microbial community succession during leaf stacking fermentation
Authors: Zhang Guanghai , Zhao Lu , Li Wei , Yao Heng , Lu Canhua , Zhao Gaokun , Liu Ziyi , Wu Yuping , Yang Wanlong , Li Yongping , Kong Guanghui
Published: February 2023

Leaf stacking fermentation involves enzymatic actions of many microorganisms and is an efficient and environmentally benign process for degrading macromolecular organic compounds. We investigated the dynamics of metabolite profiles, bacterial and fungal communities and their interactions during fermentation using cigar leaves from three geographic regions. The results showed that the contents of total sugar, reducing sugar, starch, cellulose, lignin, pectin, polyphenol and protein in cigar tobacco leaves was significantly decreased during fermentation. Notably, the furfural, neophytadiene, pyridine, benzyl alcohol, geranyl acetone, 2-butanone, 3-hydroxy-, N-hexanal, isoamylalcohol and 2,3-pentanedione were important features volatile aroma compounds during fermentation. The α-diversity of fungi and bacteria initially increased and then decreased during fermentation. The microbial diversity was influenced by fermentation stages and growing locations, in which the fermentation stages had greater impacts on the microbial diversity than locations. Microbiome profiling had identified several core bacteria includingSphingomonas, Bacillus, Staphylococcus, Pseudomonas, Ralstonia, MassiliaandFibrobacter. Fungal biomarkers includedAspergillus, Penicillium, Fusarium, CladosporiumandTrichomonascus. Interestingly, the molecular ecological networks showed that the core taxa had significant correlations with metabolic enzymes and physicochemical properties; bacteria and fungi jointly participated in the carbohydrate and nitrogen compound degrading and volatile aroma compound chemosynthesis processes during fermentation. These studies provide insights into the coupling of material conversion and microbial community succession during leaf fermentation.

IMPORTANCE

Cigar tobacco leaves are still crude after air curing. Fermentation can eliminate the pungent and bitter taste of the leaves and promote the accumulations of aromatic compounds. Hitherto, there has been no systematic study on the material conversion, metabolic enzymes and microbial community changes and their interactions in fermented leaves. The significance of our research is in identifying the potential metabolic cooperation related to microbial community, which will greatly enhance our understanding of microorganism to convert macromolecular organic to small molecules during the leaf stacking fermentation process.
Clade 2.3.4.4b H5N1 high pathogenicity avian influenza virus (HPAIV) from the 2021/22 epizootic is highly duck adapted and poorly adapted to chickens
Authors: James Joe , Billington Elizabeth , Warren Caroline J , De Sliva Dilhani , Genova Cecilia Di , Airey Maisie , Meyer Stephanie M. , Lewis Thomas , Peers-Dent Jacob , Thomas Saumya S. , Lofts Abigail , Furman Natalia , Slomka Marek J. , Brown Ian H. , Banyard Ashley C.
Published: February 2023

The 2021/2022 epizootic of high pathogenicity avian influenza (HPAIV) remains one of the largest ever in the UK, being caused by a clade 2.3.4.4b H5N1 HPAIV. This epizootic affected more than 145 poultry premises, most likely through independent incursion from infected wild birds, supported by more than 1700 individual detections of H5N1 from wild bird mortalities. Here an H5N1 HPAIV, representative of this epizootic (H5N1-21), was used to investigate its virulence, pathogenesis and transmission in layer chickens and pekin ducks, two species of epidemiological importance. We inoculated both avian species with decreasing H5N1-21 doses. The virus was highly infectious in ducks, with high infection levels and accompanying shedding of viral RNA, even in ducks inoculated with the lowest dose, reflecting the strong waterfowl adaptation of the clade 2.3.4.4 HPAIVs. Duck-to-duck transmission was very efficient, coupled with high environmental contamination. H5N1-21 was frequently detected in water sources, serving as likely sources of infection for ducks, but inhalable dust and aerosols represented low transmission risks. In contrast, chickens inoculated with the highest dose exhibited lower rates of infection compared to ducks. There was no evidence for experimental H5N1-21 transmission to any naive chickens, in two stocking density scenarios, coupled with minimal and infrequent contamination being detected in the chicken environment. Systemic viral dissemination to multiple organs reflected the pathogenesis and high mortalities in both species. In summary, the H5N1-21 virus is highly infectious and transmissible in anseriformes, yet comparatively poorly adapted to galliformes, supporting strong host preferences for wild waterfowl. Key environmental matrices were also identified as being important in the epidemiological spread of this virus during the continuing epizootic.
The hydrophobic nature of dengue 2 M residue 36 influences E protein and ApoptoM peptide
Authors: Decotter Jason , Desprès Philippe , Gadea Gilles
Published: February 2023

The recent epidemics of dengue in South West Indian Ocean coincided with the emergence of Cosmopolitan dengue virus type 2, including viral strains DES-14 in Tanzania and then RUN-18 in La Reunion. The initial step of dengue virus assembly is the formation of heterodimers between prM and E proteins where prM acts as a chaperone for E. During dengue virus maturation, prM is cleaved into membrane protein M which embeds a pro-apoptotic peptide consisting of residues 31/41 and referred as ApoptoM. An infrequent valine at position M-36 was found in DES-14 whereas RUN-18 bears a common isoleucine. Here, we investigated whether Ile-to-Val substitution at position M-36 may have an impact on RUN-18 E expression and cell-death promoting capability of RUN-18 ApoptoM. Using recombinant RUN-18 envelope proteins expressed in human epithelial A549 cells, we showed that Ile-to-Val but not Ile-to-Ala substitution affects the behavior E protein reducing the cytotoxicity of prM and E proteins. The substitution of isoleucine by valine at position M-36 leads to increase the apoptosis-inducing activity of ApoptoM. Our data highlight that hydrophobic nature of amino-acid residue in position 36 of dengue virus M protein influences E protein expression and death-promoting activity of ApoptoM opens up important perspectives in the development of effective live-attenuated DENV vaccines.
Ecological and evolutionary dynamics of cell-virus-virophage systems
Authors: Nino Barreat Jose Gabriel , Katzourakis Aris
Published: February 2023

Microbial eukaryotes can be infected by giant viruses, which can be infected by virophages. Virophages are parasites of the virus transcription machinery and can interfere with virus replication, resulting in a benefit to the eukaryotic host population. Surprisingly, virophages can integrate into the genomes of their cell or virus hosts, and have been shown to reactivate during coinfection. This raises interesting questions about the role of integration in the dynamics of cell-virus-virophage systems. Here, we use mathematical models and computational simulations to understand the effect of virophage integration on populations of cells and viruses. We also investigate programmed-cell death (PCD) and multicellularity as potential antiviral defence strategies used by cells. We found that virophages which enter the cell independently of the host virus, such as Mavirus, are expected to integrate commonly into the genomes of their cell hosts. In contrast, we show that virophages like Sputnik which form a complex with the giant virus, should rarely be found integrated in cell genomes. Alternatively, we found that Sputnik virophages can stably persist integrated in the virus population, as long as they do not completely inhibit virus replication. We also show that increasing virophage inhibition can stabilise oscillatory dynamics, which may explain the long-term persistence of viruses and virophages in the environment. Our results demonstrate that inhibition by virophages, PCD and multicellularity are effective antiviral strategies that may act in synergy against viral infection in microbial species.
callsync: an R package for alignment and analysis of multi-microphone animal recordings
Authors: Smeele Simeon Q. , Tyndel Stephen A. , Klump Barbara C. , Alarcón-Nieto Gustavo , Aplin Lucy M.
Published: February 2023

To better understand how vocalisations are used during interactions of multiple individuals, studies are increasingly deploying on-board devices with a microphone on each animal. The resulting recordings are extremely challenging to analyse, since microphone clocks drift non-linearly and record the vocalisations of non-focal individuals as well as noise.

Here we address this issue withcallsync, an R package designed to align recordings, detect and assign vocalisations to the caller, trace the fundamental frequency, filter out noise and perform basic analysis on the resulting clips.

We present a case study where the pipeline is used on a dataset of six captive cockatiels (Nymphicus hollandicus) wearing backpack microphones. Recordings initially had drift of ∼2 minutes, but were aligned to within ∼2 seconds with our package. Usingcallsync, we detected and assigned 2101 calls across three multi-hour recording sessions. Two had loud beep markers in the background designed to help the manual alignment process. One contained no obvious markers, in order to demonstrate that markers were not necessary to obtain optimal alignment. We then used a function that traces the fundamental frequency and applied spectrographic cross correlation to show a possible analytical pipeline where vocal similarity is visually assessed.

Thecallsyncpackage can be used to go from raw recordings to a clean dataset of features. The package is designed to be modular and allows users to replace functions as they wish. We also discuss the challenges that might be faced in each step and how the available literature can provide alternatives for each step.
Evolutionary conservation of mechanical strain distributions in functional transitions of protein structures
Authors: Sartori Pablo , Leibler Stanislas
Published: February 2023

One of the tenets of molecular biology is that dynamic transitions between three-dimensional structures determine the function of proteins. Therefore, it seems only natural that evolutionary analysis of proteins, presently based mainly on their primary sequence, needs to shift its focus towards their function as assessed by corresponding structural transitions. This can be facilitated by recent progress in cryogenic electron microscopy that provides atomic structures of multiple conformational states for proteins and protein assemblies isolated from evolutionarily related species. In this work, we study evolutionary conservation of multi-protein assembly function by using mechanical strain as a quantitative footprint of structural transitions. We adopt the formalism of finite strain analysis, developed in condensed matter physics, and apply it, as a case study, to a classical multi-protein assembly, the ATP synthase. Our Protein Strain Analysis (PSA) provides a precise characterization of rotation domains that agrees with the present biophysical knowledge. In addition, we obtain a strain distribution on the protein structure associated with functional transitions. By analyzing in detail, the strain patterns of the chains responsible for ATP synthesis across distinct species, we show that they are evolutionarily conserved for the same functional transition. Such conservation is not revealed by displacement or rotation patterns. Furthermore, within each functional transition, we can identify conserved strain patterns for ATP synthases isolated from different organisms. The observed strain conservation across evolutionary distant species indicates that strain should be essential in future structure-based evolutionary studies of protein function.
A cingulate-hippocampal circuit mediates early depressive symptoms in Alzheimer’s disease
Authors: Chen Yanbing , Peng Huimin , Zhuang Kai , Xie Wenting , Li Chenli , Xue Jin , Chen Meiqin , Huang Xiaoting , Zou Tingting , Wang Ya , Can Dan , Li Huifang , Yuan Tifei , Zhang Jie
Published: February 2023

Abstract

Depressive symptoms are prevalent and precedes cognitive decline in Alzheimer’s disease (AD), which worsen the clinical outcome and severely challenge the life quality of the patients. However, the neural circuitry mediating mood disturbance in AD remains elusive. Here we report that the glutamatergic projection from the anterior cingulate cortex (ACC) to the ventral hippocampal CA1 (vCA1) acts as the neural substrate of depressive symptoms in AD. We systemically mapped axonal projection in early stage of 5xFAD mice (3 months), which accompanies depressive- like behavior in these animals and identified reduced axonal projection from ACC to vCA1. This is in accordance with reduced axonal calcium signals detected with in vivo fiber photometry. Chemogenetic or optogenetic reversal of ACC-vCA1 circuitry activity efficiently ameliorated the depressive-like behaviors as well as cognitive impairment in 5xFAD mice. We further identified the synaptic molecules neuregulin-1 (Nrg1) as one vital signal regulating the synaptic glutamate transmission from the ACC to the vCA1. Collectively, these results indicated ACC-vCA1 as a critical pathway that regulates emotional states in Alzheimer’ disease. Targeting cingulate cortices with brain stimulation may treat depression in AD.
A very-low carbohydrate content in a high-fat diet modifies the plasma metabolome and alleviates experimental atherosclerosis
Authors: Castro R , Kalecký K , Huang NK , Petersen K , Singh V , Ross AC , Neuberger T , Bottiglieri T
Published: February 2023

Ketogenic diets (KD) are very low-carbohydrate diets that promote nutritional ketosis and are widely used for weight loss, although concerns about potential adverse cardiovascular effects remain. In this study, we used apolipoprotein E deficient (ApoE-/-)mice to investigate the vascular impact and plasma metabolic signature of a very high-fat KD compared to a non-ketogenic high-fat diet (HFD). Plasma samples were collected after 4, 8, and 12 weeks on the experimental diets and used to quantify the major ketone body β-hydroxybutyrate (BHB), inflammatory cytokines (interleukin 6, IL-6; monocyte chemoattractant protein 1, MCP-1; and tumor necrosis factor α, TNF-α), and targeted metabolomic profiling by mass spectrometry. Moreover, aortic atherosclerotic lesions were quantified ex vivo by magnetic resonance imaging (MRI) on a 14-tesla system. The results showed that, relative to HFD mice, the KD mice had markedly higher levels of BHB and lower levels of cytokines, confirming the presence of ketosis that alleviated the well-established fat-induced systemic inflammation. Moreover, mice under nutritional ketosis displayed a distinct plasma amino acid profile evidencing a KD-induced alteration in protein metabolism. Significant changes in the plasma metabolome in KD mice included a decrease in lipophilic and increase in hydrophilic metabolites. Despite the higher fat content of the KD versus the HFD, KD mice presented significantly lower levels of several lipid metabolites, including phosphatidylcholines, cholesterol esters, sphingomyelins, and ceramides. Consistent with the shift in energy metabolism toward fatty acid oxidation caused by the KD, the ratio of acylcarnitines to free carnitine was significantly higher in KD than in HFD mice., the aortic plaque burden was significantly lower in the KD versus the HFD group. In conclusion, nutritional ketosis induced by the KD was associated with specific metabolic changes and an atheroprotective phenotype versus the HFD.
Synthesis, crystal structure and Hirshfeld surface analysis of di-μ2-iodido-bis[(2,2′-biquinoline-κ2
N,N′)copper(I)]
Authors: Temesgen Ayalew W. , Novikov Anton P. , Tskhovrebov Alexander G. , Kultyshkina Ekaterina K. , Le Tuan Anh
Published: February 2023

The molecular and crystal structures of the title compound, [Cu2I2(C18H12N2)2], were examined by single-crystal X-ray diffraction and Hirshfeld surface analysis. The Cu atom is coordinated in a distorted tetrahedral geometry by two N atoms from the 2,2′-biquinoline ligands and the two μ2-bridging iodide ligands. The molecules are in contact via π–π-stacking interactions. Hirshfeld surface analysis showed that the most important contributions to the intermolecular interactions are H...H (39.7%), H...I/I...H (17.8%), C...H/H...C (17.5%), C...C (16.5%), N...C/C...N (3.9%) and N...H/H...N (3.5%).
A periodic-like table of space groups
Authors: Kahr Bart
Published: February 2023

There are about 100 chemical elements, and 200 space groups, rounding to the nearest hundreds. The elements, by virtue of the iconic periodic table, which hangs in schoolrooms worldwide, are part of our common culture. Few on the outside of solid-state science and discrete mathematics know of the remarkable enumeration of the space groups and how they organize solids, the chemical elements included, that can be conformed to translationally periodic lattices in three dimensions. Perhaps the comparative inaccessibility of space groups to non-specialists can be attributed to the absence of a single chart that captures and organizes the space groups in a glance, as does the periodic table for the chemical elements? Here is designed a periodic-like table of the space groups. The symmorphic space groups are organized as the coordinates of two non-linear, non-orthogonal axes that capture the point group symmetry and the order of the group, the multiplicity of general positions. The related non-symmorphic groups are treated as `isotopes' of the symmorphic groups and are enumerated with a subscript. The intent is to inspire better designs and to bring the crystallographic space groups to the attention of a wider audience.
Co-worker incivility and employee engagement among Ghanaian bank workers: does emotional intelligence matter?
Authors: Amponsah-Tawiah Kwesi , Baafi Nana Kojo Ayimadu , Mensah Jusice
Published: February 2023

Purpose

The purpose of this study is to ascertain the mechanism through which an employee engages at the workplace when faced with an uncivil act.

Design/methodology/approach

The study adopted a cross-sectional survey design to sample 482 participants drawn from commercial banks operating in Ghana. The population of the study (employees working in banks in Ghana) was selected owing to the recent reforms in the sector coupled with the emerging fear of loss of jobs as a result of the corona virus pandemic and the potential impact on employee work attitudes. Participants were however selected conveniently and employees who were available and willing to participate given questionnaires to complete.

Findings

Co-worker incivility significantly and negatively predicted employee engagement, while emotional intelligence (EI) predicted employee engagement positively. Furthermore, EI served as a mediator between co-worker incivility and engagement.

Research limitations/implications

Despite these encouraging findings, the mechanism underlying these effects could not be identified. Therefore, future studies can establish the underlying mechanisms of these effects by using qualitative studies or the mixed-method. Future studies can also explore other personal resources such as psychological capital or personality traits in mitigating the negative effects of workplace incivility.

Practical implications

Given the fact that incivility has a significant negative influence on employees within the organisation, there is the need for government and policy makers to enact an inclusive policy that deals with employee mistreatments and most especially low key mistreatment. This could be done through the promulgation of a national policy on psychosocial risk management (PRIMA) as most of the uncivil acts in organisations present as psychosocial risk factors. Secondly, at the organisational level there is the need to consider EI of employees most especially when recruiting employees so as to avoid squared pegs being placed in round holes.

Originality/value

This research found out that for an employee to engage or not when faced with an uncivil act, one’s EI has to play a role. The appraisal theory was used to provide a sufficient grounds in exploring the role of EI in the evaluations and determination of occurrences in organisations as intentional or unintentional, positive or negative and hence the resultant work outcomes.
Authentic leadership’s influence on strategic corporate social responsibility in South Africa: mediated by participative decision-making
Authors: Nqumba Bradley Majil’andile , Scheepers Caren Brenda
Published: February 2023

Purpose

The purpose of this paper is to investigate the influence of authentic leadership on strategic corporate social responsibility (CSR) in a less researched environment. This study set out to fill that gap in researching the direct influence of employees’ perceptions about the authenticity of their leaders as well as indirect effect through participative decision-making on strategic CSR which means the genuine intention to benefit society.

Design/methodology/approach

A quantitative research approach was followed, with an online survey to employees in large South African corporations across various industries that were mostly more than 10 years old. There were 1,417 useable questionnaires. Structural equation modelling was used to test proposed hypotheses of mediation effects.

Findings

The results revealed that authentic leadership has a significant indirect effect through participative decision-making on employees’ perceptions around strategic CSR – that is, whether their corporations are genuinely socially and environmentally responsible.

Research limitations/implications

The data collected were cross-sectional, and survey-based in the South African corporate environment; therefore, limited generalisations can be made, and causality could not be claimed.

Practical implications

Authentic leadership and participative decision-making are required to significantly influence employees’ perceptions about companies’ genuine interest in benefiting external stakeholders. Consistency between leaders’ words and deeds is important for employees, and therefore, companies must be socially responsible towards employees.

Originality/value

The main contribution of this research lies in showing that perception of leaders’ authenticity was enhanced when employees were allowed to participate in decision-making, which then increased positive perceptions about the organisation’s CSR focus. The study highlights similarities between authentic leadership and the African humanism philosophy of Ubuntu.
Analysis of hydrothermal performance for laminar forced convective flow through a wavy channel with porous blocks
Authors: Mehta Sumit Kumar , Pati Sukumar
Published: February 2023

Purpose

The purpose of this paper is to investigate computationally the hydrothermal characteristics for forced convective laminar flow of water through a channel with a top wavy wall and a flat bottom wall having metallic porous blocks.

Design/methodology/approach

The governing equations are solved computationally using a finite element method–based numerical solver COMSOL Multiphysics® for the following range of parameters: 10 ≤ Reynolds number (Re) ≤ 500 and 10–4 ≤ Darcy number (Da) ≤ 10–1.

Findings

The presence of porous blocks significantly influences the heat transfer rate, and the value of local Nusselt number increases with the increase in Da. The value of the average Nusselt number decreases with Da for the top wall and the same is enhanced for the bottom wall of the wavy channel with porous blocks (WCPB). The value of the average Nusselt number for WCPB is significantly higher than that of the wavy channel without porous block (WCWPB), plane channel without porous block (PCWPB) and plane channel with the porous block (PCPB) at higher Re. For PCPB, the performance factor (PF) is always higher than that of WCWPB and WCPB for Da = 10–4 and Da = 10–3. Also, PF for WCPB is higher than that of WCWPB for higher Re except for Da = 10–4. Further, the value of for WCPB is higher than that of PCPB at Da = 10–2 and 10–1 at Re = 500.

Practical implications

The current study is useful in designing efficient heat exchangers for process plants, solar collectors and aerospace applications.

Originality/value

The analysis of thermo-hydraulic characteristics for laminar flow through a channel with a top wavy wall and a flat bottom wall having metallic porous blocks have been analyzed for the first time. Further, a comparative assessment of the performance has been performed with a wavy channel without a porous block, a plane channel without a porous block and a plane channel with porous blocks.
Tour guides’ self-efficacy and resilience capability building through sharing economy platforms
Authors: Shang Kaiti , Fan Daisy X.F. , Buhalis Dimitrios
Published: February 2023

Purpose

This study aims to explore how the local tour guides (LTGs) operate through the sharing economy platform. This study explores how LTGs have responded to the COVID-19 pandemic restrictions using self-efficacy and other resources to improve resilience and performance. This study also delineates the working mechanisms of peer-to-peer (P2P) platform-enabled, dynamic capability building processes, in the tourism sharing economy.

Design/methodology/approach

This research adopted an interpretive approach to understand the focal phenomenon using two types of data. A total of 40 semi-structured interviews with LTGs and 26,478 online tourist reviews from tour guide service participants’ before and during the COVID-19 pandemic were used.

Findings

The findings of this study revealed that LTGs used sharing economy platforms to arrange flexible tour guide services. Resilience emerged through dynamic capability that addressed contextual factors in real time. LTGs coordinated different resources and customers during a time of uncertainty. Different sources of self-efficacy and types of dynamic capability were identified. The interplay between LTGs’ self-efficacy and dynamic capability was also delineated.

Practical implications

The findings provide guidance for LTGs on P2P platforms and other sharing economy sectors on how diverse resources enabled by the sharing economy can enhance resilience during times of uncertainty. LTGs that engage with contextual information and are dynamic can adopt itineraries and services that will benefit tourists and their business.

Originality/value

This study contributes to the sharing economy literature by theorizing the working flow that enables LTGs to exert self-efficacy and leverage dynamic capability on P2P platforms. This study also contributes by linking resilience to contextual factors in real time. The outcomes provide guidance for LTGs to remain competitive and establish resilience in uncertain environments.