bluuebunny/crossref_metadata_2025 huggingface dataset:
LOCOM: A logistic regression model for testing differential abundance in compositional microbiome data with false discovery rate control
Authors: Hu Yingtian , Satten Glen A. , Hu Yi-Juan
Published: October 2021

Motivation

Compositional analysis is based on the premise that a relatively small proportion of taxa are “differentially abundant”, while the ratios of the relative abundances of the remaining taxa remain unchanged. Most existing methods of compositional analysis such as ANCOM or ANCOM-BC use log-transformed data, but log-transformation of data with pervasive zero counts is problematic, and these methods cannot always control the false discovery rate (FDR). Further, high-throughput microbiome data such as 16S amplicon or metagenomic sequencing are subject to experimental biases that are introduced in every step of the experimental workflow. McLaren, Willis and Callahan [1] have recently proposed a model for how these biases affect relative abundance data.

Methods

Motivated by [1], we show that the (log) odds ratios in a logistic regression comparing counts in two taxa are invariant to experimental biases. With this motivation, we propose LOCOM, a robust logistic regression approach to compositional analysis, that does not require pseudocounts. We use a Firth bias-corrected estimating function to account for sparse data. Inference is based on permutation to account for overdispersion and small sample sizes. Traits can be either binary or continuous, and adjustment for continuous and/or discrete confounding covariates is supported.

Results

Our simulations indicate that LOCOM always preserved FDR and had much improved sensitivity over existing methods. In contrast, ANCOM often had inflated FDR; ANCOM-BC largely controlled FDR but still had modest inflation occasionally; ALDEx2 generally had low sensitivity. LOCOM and ANCOM were robust to experimental biases in every situation, while ANCOM-BC and ALDEx2 had elevated FDR when biases at causal and non-causal taxa were differentially distributed. The flexibility of our method for a variety of microbiome studies is illustrated by the analysis of data from two microbiome studies.

Availability and implementation

Our R package LOCOM is available on GitHub athttps://github.com/yijuanhu/LOCOMin formats appropriate for Macintosh or Windows.
Clinical utility of Elecsys Anti-SARS-CoV-2 S assay in COVID-19 vaccination: An exploratory analysis of the mRNA-1273 phase 1 trial
Authors: Jochum Simon , Kirste Imke , Hortsch Sayuri , Grunert Veit Peter , Legault Holly , Eichenlaub Udo , Kashlan Basel , Pajon Rolando
Published: October 2021

Background

The ability to quantify an immune response after vaccination against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is essential. This study assessed the clinical utility of the quantitative Roche Elecsys® Anti-SARS-CoV-2 S assay (ACOV2S) using samples from the 2019-nCoV vaccine (mRNA-1273) phase 1 trial (NCT04283461).

Methods

Samples from 30 healthy participants, aged 18–55 years, who received two injections with mRNA-1273 at a dose of 25 μg (n=15) or 100 μg (n=15), were collected at Days 1 (first vaccination), 15, 29 (second vaccination), 43 and 57. ACOV2S results (shown in U/mL – equivalent to BAU/mL per the first WHO international standard) were compared with results from ELISAs specific to antibodies against the Spike protein (S-2P) and the receptor binding domain (RBD) as well as neutralization tests including nanoluciferase (nLUC80), live-virus (PRNT80), and a pseudovirus neutralizing antibody assay (PsVNA50).

Results

RBD-specific antibodies were already detectable by ACOV2S at the first time point of assessment (d15 after first vaccination), with seroconversion before in all but 2 participants (25 μg dose group); all had seroconverted by Day 29. Across all post-baseline visits, geometric mean concentration of antibody levels were 3.27–7.48-fold higher in the 100 μg compared with the 25 μg dose group. ACOV2S measurements were highly correlated with those from RBD ELISA (Pearson’s r=0.938; p<0.0001) and S-2P ELISA (r=0.918; p<0.0001). For both ELISAs, heterogeneous baseline results and smaller increases in antibody levels following the second vs first vaccination compared with ACOV2S were observed. ACOV2S showed absence of any baseline noise indicating high specificity detecting vaccine-induced antibody response. Moderate–strong correlations were observed between ACOV2S and neutralization tests (nLUC80 r=0.933; PsVNA50, r=0.771; PRNT80, r=0.672; all p≤0.0001).

Conclusion

The Elecsys Anti-SARS-CoV-2 S assay (ACOV2S) can be regarded as a highly valuable method to assess and quantify the presence of RBD-directed antibodies against SARS-CoV-2 following vaccination, and may indicate the presence of neutralizing antibodies. As a fully automated and standardized method, ACOV2S could qualify as the method of choice for consistent quantification of vaccine-induced humoral response.
Ptbp1 deletion does not induce glia-to-neuron conversion in adult mouse retina and brain
Authors: Hoang Thanh , Kim Dong Won , Appel Haley , Pannullo Nicole A. , Leavey Patrick , Ozawa Manabu , Zheng Sika , Yu Minzhong , Peachey Neal S. , Kim Juhyun , Blackshaw Seth
Published: October 2021

Direct reprogramming of glia into neurons is a potentially promising approach for the replacement of neurons lost to injury or neurodegenerative disorders. Knockdown of the polypyrimidine tract-binding protein Ptbp1 has been recently reported to induce efficient conversion of retinal Müller glia and brain astrocytes into functional neurons. However, genetic analysis of Ptbp1 function in adult glia has not been conducted. Here, we use a combination of genetic lineage tracing, scRNA-Seq, and electrophysiological analysis to show that specific deletion of Ptbp1 in adult retinal Müller glia and brain astrocytes does not lead to any detectable level of glia-to-neuron conversion. Only a few changes in gene expression are observed in glia following Ptbp1 deletion, and glial identity is maintained. These findings highlight the importance of using genetic manipulation and lineage tracing methods in studying cell type conversion.
Projected dynamics of breeding habitat suitability for a steppe-land bird warrant anticipatory conservation actions
Authors: Simoncini Andrea , Ramellini Samuele , Martineau Alexis , Massolo Alessandro , Giunchi Dimitri
Published: October 2021

Understanding spatial and temporal variations of habitat suitability is fundamental for species’ conservation under global change. Steppic species are particularly sensitive to anthropogenic change and have undergone large declines in the last decades. We aimed to describe current and future breeding habitat suitability for the Eurasian stone-curlew Burhinus oedicnemus, a steppic species of conservation concern, and to identify critical areas for its conservation. We collected 1628 presence records covering the period 1992-2016. We developed a species distribution model using a dynamic Maxent algorithm and a set of pseudo-absences with a spatial density weighted on a fixed kernel density estimated on the presences, to mitigate the potential sampling bias. We projected this model under a set of carbon emission, socioeconomic and land-use/land-cover scenarios for the years 2030, 2050, 2070 and 2090. Finally, we described the cell-wise and mean change of breeding habitat suitability through consecutive time intervals and identified the areas critical for the species’ conservation.

All scenarios predicted a short-term northward shift of suitable areas, followed by a period of stability. We found no consistent trends in the mean change of breeding habitat suitability, and similar extents of suitable areas under current and future scenarios. Critical areas for the conservation of the species are mainly located in Northern Europe, Israel and parts of North Africa, the Iberian Peninsula and Italy. According to our results, the Eurasian stone-curlew has the potential to maintain viable populations in the Western Palearctic, but dispersal limitations might hinder the colonization of shifted suitable areas. Targeted conservation interventions in the critical areas are therefore recommended to secure the future of the species under global change.
Using bootstrap procedures for testing the modular partition inferred via leading eigenvector community detection algorithm
Authors: Vertsimakha Oksana , Dzeverin Igor
Published: October 2021

Modularity and modular structures can be recognized at various levels of biological organization and in various domains of studies. Recently, algorithms based on network analysis came into focus. And while such a framework is a powerful tool in studying modular structure, those methods usually pose a problem of assessing statistical support for the obtained modular structures. One of the widely applied methods is the leading eigenvector, or Newman’s spectral community detection algorithm. We conduct a brief overview of the method, including a comparison with some other community detection algorithms and explore a possible fine-tuning procedure. Finally, we propose an adapted bootstrap-based procedure based on Shimodaira’s multiscale bootstrap algorithm to derive approximately unbiased p-values for the module partitions of observations datasets. The proposed procedure also gives a lot of freedom to the researcher in constructing the network construction from the raw numeric data, and can be applied to various types of data and used in diverse problems concerning modular structure. We provide an R language code for all the calculations and the visualization of the obtained results for the researchers interested in using the procedure.
Protection against avian coronavirus conferred by oral vaccination with live bacteria secreting LTB-fused viral proteins
Authors: Lublin Avishai , Katz Chen , Gruzdev Nady , Yadid Itamar , Bloch Itai , Farnoushi Yigal , Simanov Luba , Berkovitz Asaf , Elyahu Dalia , Pitcovskib Jacob , Shahar Ehud
Published: October 2021

The devastating impact of infectious bronchitis (IB) triggered by the IB virus (IBV), on poultry farms is generally curbed by livestock vaccination with live attenuated or inactivated vaccines. Yet, this approach is challenged by continuously emerging variants and by time limitations of vaccine preparation techniques. This work describes the design and evaluation of an anti-IBV vaccine comprised ofE. coliexpressing and secreting viral spike 1 subunit (S1) and nucleocapsid N-terminus and C-terminus polypeptides fused to heat-labile enterotoxin B (LTB) (LS1, LNN, LNC, respectively). Following chicken oral vaccination, anti-IBV IgY levels and cellular-mediated immunity as well as protection against virulent IBV challenge, were evaluated 14 days following the booster dose. Oral vaccination induced IgY levels that exceeded those measured following vaccination with each component separately. Following exposure to inactivated IBV, splenocytes isolated from chicks orally vaccinated with LNN or LNC -expressing bacteria, showed a higher percentage of CD8+cells as compared to splenocytes isolated from chicks vaccinated with wild type or LTB-secretingE. coliand to chicks subcutaneously vaccinated. Significant reduction in viral load and percent of shedders in the vaccinated chicks was evident starting 3 days following challenge with 107.5EID50/ml virulent IBV. Taken together, orally delivered LTB-fused IBV polypeptide-expressing bacteria induced virus-specific IgY antibody production and was associated with significantly shorter viral shedding on challenge with a live IBV. The proposed vaccine design and delivery route promise an effective and rapidly adaptable means of protecting poultry farms from devastating IB outbreaks.

Highlights

Mucosal vaccination was shown particularly beneficial against respiratory viruses.

An anti-IBV vaccine composed of three IBV polypeptides fused to LTB was designed.

Vaccine composed of bacteria secreting polypeptides was orally delivered.

Vaccine induced specific immune responses and shortened viral shedding duration.
Functional interaction between Drosophila olfactory sensory neurons and their support cells
Authors: Prelic Sinisa , Mahadevan Venkatesh Pal , Venkateswaran Vignesh , Lavista-Llanos Sofia , Hansson Bill S. , Wicher Dieter
Published: October 2021

Insects detect volatile chemicals using antennae, which house a vast variety of olfactory sensory neurons (OSNs) that innervate hair-like structures called sensilla where odor detection takes place. In addition to OSNs, the antenna also hosts various support cell types. These include the triad of trichogen, tormogen and thecogen support cells that lie adjacent to their respective OSNs. The arrangement of OSN supporting cells occurs stereotypically for all sensilla and is widely conserved in evolution. While insect chemosensory neurons have received considerable attention, little is known about the functional significance of the cells that support them. For instance, it remains unknown whether support cells play an active role in odor detection, or only passively contribute to homeostasis, e.g. by maintaining sensillum lymph composition. To investigate the functional interaction between OSNs and support cells, we used optical and electrophysiological approaches in Drosophila. First, we characterized the distribution of various supporting cells using genetic markers. By means of an ex vivo antennal preparation and genetically-encoded Ca2+ and K+ indicators, we then studied the activation of these auxiliary cells during odor presentation in adult flies. We observed acute responses and distinct differences in Ca2+ and K+ fluxes between support cell types. Finally, we observed alterations in OSN responses upon thecogen cell ablation in mature adults. Upon inducible ablation of thecogen cells, we notice a gain in mechanical responsiveness to mechanical stimulations during single-sensillum recording, but a lack of change to neuronal resting activity. Taken together, these results demonstrate that support cells play a more active and responsive role during odor processing than previously thought. Our observations thus reveal that support cells functionally interact with OSNs and may be important for the extraordinary ability of insect olfactory systems to dynamically and sensitively discriminate between odors in the turbulent sensory landscape of insect flight.
A class of identifiable phylogenetic birth-death models
Authors: Legried Brandon , Terhorst Jonathan
Published: October 2021

In a striking result, Louca and Pennell (2020) recently proved that a large class of phylogenetic birth-death models are statistically unidentifiable from lineage-through-time (LTT) data: any pair of sufficiently smooth birth and death rate functions is “congruent” to an infinite collection of other rate functions, all of which have the same likelihood for any LTT vector of any dimension. As Louca and Pennell argue, this fact has distressing implications for the thousands of studies that have utilized birth-death models to study evolution.

In this paper, we qualify their finding by proving that an alternative and widely used class of birth-death models is indeed identifiable. Specifically, we show that piecewise constant birth-death models can, in principle, be consistently estimated and distinguished from one another, given a sufficiently large extant time tree and some knowledge of the present-day population. Subject to mild regularity conditions, we further show that any unidentifiable birth-death model class can be arbitrarily closely approximated by a class of identifiable models. The sampling requirements needed for our results to hold are explicit, and are expected to be satisfied in many contexts such as the phylodynamic analysis of a global pandemic.
Trans-epithelial migration is essential for neutrophil activation during RSV infection
Authors: Robinson Elisabeth , Herbert Jenny Amanda , Palor Machaela , Ren Luo , Larken Isobel , Patel Alisha , Moulding Dale , Cortina-Borja Mario , Smyth Rosalind Louise , Smith Claire Mary
Published: October 2021

The recruitment of neutrophils to the infected airway occurs early following respiratory syncytial virus (RSV) infection and high numbers of activated neutrophils in airway and blood is associated with the development of severe disease. Here, we investigated whether trans-epithelial migration across primary human airway epithelial cells (AECs) is sufficient and necessary for neutrophil activation during RSV infection. Using flow cytometry, we identified three populations of neutrophils in our in vitro model; those in suspension in basolateral and apical compartments and those that migrated and adhered to AECs. After 1h incubation, the number of adherent neutrophils was significantly greater following RSV infection compared to mock infected. We found that, when migration occurred, neutrophil expression of CD11b, CD62L, CD64, NE and MPO increased in all compartments. However, this did not occur when neutrophils were prevented from migrating. This suggests that the heightened neutrophil activation we detected in the basolateral compartment may be due to reverse migrating neutrophils, as has been suggested by clinical observations. Using live-cell fluorescent microscopy, we then profiled the early temporal and spatial movement and adherence of human neutrophils during migration. Our findings suggest three main phases of early neutrophil recruitment and behaviour in the airways during RSV infection, with neutrophil recruitment, activation and adherence to RSV infected AECs, with clustering, occurring within the first 20 minutes. This work and the model we developed could provide new insight into how neutrophil activation and a dysregulated neutrophil response to RSV mediates disease severity.

Graphical Abstract

Building on previous work of neutrophil function we propose 3 main phases of early neutrophil recruitment and behaviour in the airways during RSV infection. Phase 1. Initial chemotaxis and adherence: Here unstimulated circulating neutrophils expressing baseline levels of CD11b migrate across infected AECs in response to chemotactic signals in the apical supernatant. Some neutrophils remain adherent to the infected AECs. Phase 2: Activation and reverse migration: once on the apical side of the epithelium, neutrophils increase expression of CD11b and other activation associated markers, and some ‘activated’ neutrophils undergo reverse migration. Neutrophils with greater expression of CD11b are detected on the basolateral side Phase 3: Amplified chemotaxis and clustering: after 20 minutes, adherent neutrophils begin to rapidly cluster on RSV infected primary airway epithelial cells cultures, mediated by signalling from a dying neutrophil. Drawing created using BioRender.com.
Brain State-Dependent Modulation of Thalamic Visual Processing by Cortico-thalamic Feedback
Authors: Reinhold Kimberly , Resulaj Arbora , Scanziani Massimo
Published: October 2021

The behavioral state of a mammal impacts how the brain responds to visual stimuli as early as in the dorsolateral geniculate nucleus of the thalamus (dLGN), the primary relay of visual information to the cortex. A clear example of this is the markedly stronger response of dLGN neurons to higher temporal frequencies of the visual stimulus in alert as compared to quiescent animals. The dLGN receives strong feedback from the visual cortex, yet whether this feedback contributes to these state-dependent responses to visual stimuli is poorly understood. Here we show that in mice, silencing cortico-thalamic feedback abolishes state-dependent differences in the response of dLGN neurons to visual stimuli. This holds true for dLGN responses to both temporal and spatial features of the visual stimulus. These results reveal that the state-dependent shift of the response to visual stimuli in an early stage of visual processing depends on cortico-thalamic feedback.
Temperature impacts on fish physiology and resource abundance lead to faster growth but smaller fish sizes and yields under warming
Authors: Lindmark Max , Audzijonyte Asta , Blanchard Julia , Gårdmark Anna
Published: October 2021

Resolving the combined effect of climate warming and exploitation in a food web context is key for predicting future biomass production, size-structure, and potential yields of marine fishes. Previous studies based on mechanistic size-based food web models have found that bottom-up processes are important drivers of size-structure and fisheries yield in changing climates. However, we know less about the joint effects of ‘bottom-up’ and physiological effects of temperature; how do temperature effects propagate from individual-level physiology through food webs and alter the size-structure of exploited species in a community? Here we assess how a species-resolved size-based food web is affected by warming through both these pathways, and by exploitation. We parameterize a dynamic size spectrum food web model inspired by the offshore Baltic Sea food web, and investigate how individual growth rates, size-structure, relative abundances of species and yields are affected by warming. The magnitude of warming is based on projections by the regional coupled model system RCA4-NEMO and the RCP 8.5 emission scenario, and we evaluate different scenarios of temperature dependence on fish physiology and resource productivity. When accounting for temperature-effects on physiology in addition to on basal productivity, projected size-at-age in 2050 increases on average for all fish species, mainly for young fish, compared to scenarios without warming. In contrast, size-at-age decreases when temperature affects resource dynamics only, and the decline is largest for young fish. Faster growth rates due to warming, however, do not always translate to larger yields, as lower resource carrying capacities with increasing temperature tend to result in declines in the abundance of larger fish and hence spawning stock biomass. These results suggest that to understand how global warming affects the size structure of fish communities, both direct metabolic effects and indirect effects of temperature via basal resources must be accounted for.
Sequential Temporal Anticipation Characterized by Neural Power Modulation and in Recurrent Neural Networks
Authors: Teng Xiangbin , Zhang Ru-Yuan
Published: October 2021

Relevant prospective moments arise intermittently, while most of time is filled with irrelevant events, or noise, that constantly bombard our sensory systems. Thus, anticipating a few key moments necessitates disregarding what lies between the present and the future – the noise. Here, through examining how the brain and the recurrent neural networks (RNNs) anticipate a sequence of prospective moments without relying on any external timing cues, we provided a reinterpretation of temporal anticipation. We first designed a “premembering” task, where we marked three temporal locations in white noise and asked human listeners to detect a tone at one of these points. Using power modulation analyses, we investigated the memory-guided anticipatory processes in trials involving only flat noise. Our research revealed a unique neural-power modulation pattern for sequential temporal anticipation: neural power within the alpha-beta band range fluctuates over time, accurately identifying the marked locations on a sub-second scale and correlating with tone detection performance. To understand the functional roles of these neural modulations, we utilized RNNs optimized for the behavioral task. The hidden dynamics of the RNNs mirrored the neural modulations, and additional analyses and perturbations on the RNNs indicated that the neural power modulations in the alpha-beta band resulted from selective suppression of irrelevant noise periods and heightened sensitivity to anticipated temporal locations. Our behavioral, neural, and modeling findings collectively indicate that sequential temporal anticipation involves a process of dynamic gain control: anticipating a few significant moments involves actively disregarding irrelevant events that frequently occur.
Pioglitazone administration restores a PPARG-dependent transcriptional network and ATP levels within skeletal muscles of mice implanted with patient-derived breast tumors
Authors: Stanton David A. , Wilson Hannah E. , Chapa Matthew G. , Link Jessica N. , Geldenhuys Werner , Pistilli Emidio E.
Published: October 2021

Background

Fatigue is common in patents with breast cancer (BC), and can occur in patients with early stage disease and in the absence of muscle wasting (i.e. cachexia). We have reported transcriptional and proteomic alterations in muscles from BC patients, which are associated with fatigue. Mice implanted with human BC xenografts recapitulate the muscle molecular composition changes seen in patients, coupled with a greater rate of contraction-induced fatigue. Multiple bioinformatics platforms in both human and mouse muscles have identified peroxisome proliferator activated receptor gamma (PPARG) as central to this phenotype, with multiple PPARG target genes downregulated in response to tumor growth. The current study tested the hypothesis that the PPARG agonist pioglitazone (pio), a commonly prescribed diabetes drug, would rescue the transcriptional alterations observed in muscles of tumor-bearing mice.

Methods

Sixteen female NSG mice were implanted with breast cancer patient-derived orthotopic xenografts (BC-PDOX) via transplantation of Her2/neu+human tumor fragments. BC-PDOX mice were randomly assigned to a treatment group that received daily oral pio at 30 mg.kg-1(n=8), or a control group that received a similar volume of vehicle (n=8). Treatment was initiated when tumors reached a volume of 600mm3, and lasted for 2-weeks. Hindlimb muscles were isolated from BC-PDOX and non-tumor bearing mice for RNA-sequencing, gene expression validation, and ATP quantification. Differentially expressed genes (DEGs) in muscles from BC-PDOX mice relative to non-tumor bearing controls were identified using DESeq2, and multiple bioinformatics platforms were employed to contextualize the DEGs.

Results

We found that the administration of pio restored the muscle gene expression patterns of BC-PDOX mice to a profile resembling muscles of non-tumor bearing NSG control mice. Validation of skeletal muscle gene expression by qPCR confirmed pio increased the expression of PPARG target genes in skeletal muscles. Isolated mitochondria from muscles of BC-PDOX mice treated with pio contained greater levels of ATP. There were no differences in body weights, muscle weights, or tumor volumes in pio vs. vehicle treated BC-PDOX mice.

Conclusions

These data demonstrate that oral pio supplementation rescues the BC-associated downregulation of PPARG target genes in skeletal muscle. Additionally, muscles from BC-PDOX mice treated with pio had greater levels of ATP, which would be associated a more fatigue-resistant muscle phenotype. Therefore, we propose that the FDA-approved and generic diabetes drug, pio, be considered as a supportive therapy for the treatment of BC-associated muscle fatigue.
RecA and RecB: probing complexes of DNA repair proteins with mitomycin C in live Escherichia coli with single-molecule sensitivity
Authors: Payne-Dwyer Alex L. , Syeda Aisha H. , Shepherd Jack W. , Frame Lewis , Leake Mark. C.
Published: October 2021

The RecA protein and RecBCD complex are key bacterial components for the maintenance and repair of DNA. RecBCD is a helicase-nuclease that uses homologous recombination to resolve double-stranded DNA breaks. It also facilitates coating of single-stranded DNA with RecA to form RecA filaments, a vital step in the double-stranded break DNA repair pathway. However, questions remain about the mechanistic roles of RecA and RecBCD in live cells. Here, we use millisecond super-resolved fluorescence microscopy to pinpoint the spatial localization of fluorescent reporters of RecA or RecB at physiological levels of expression in individual live Escherichia coli cells. By introducing the DNA crosslinker mitomycin C, we induce DNA damage and quantify the resulting steady state changes in stoichiometry, cellular protein copy number and molecular mobilities of RecA and RecB. We find that both proteins accumulate in molecular hotspots to effect repair, resulting in RecA stoichiometries equivalent to several hundred molecules that assemble largely in dimeric subunits before DNA damage, but form periodic subunits of approximately 3-4 molecules within mature filaments of several thousand molecules. Unexpectedly, we find that the physiologically predominant forms of RecB are not only rapidly diffusing monomers, but slowly diffusing dimers.
A mitochondrial electron transport chain with atypical subunit composition confers oxygen sensitivity to a mammalian chemoreceptor
Authors: Timón-Gómez Alba , Scharr Alexandra L. , Wong Nicholas Y. , Ni Erwin , Roy Arijit , Liu Min , Chau Julisia , Lampert Jack L. , Hireed Homza , Kim Noah S. , Jan Masood , Gupta Alexander R. , Day Ryan W. , Gardner James M. , Wilson Richard J. A. , Barrientos Antoni , Chang Andy J.
Published: October 2021

The carotid body (CB) is the major chemoreceptor for blood oxygen in the control of ventilation in mammals, contributing to physiological adaptation to high altitude, pregnancy, and exercise, and its hyperactivity is linked to chronic conditions such as sleep-disorder breathing, hypertension, chronic heart failure, airway constriction, and metabolic syndrome (1–3). Upon acute hypoxia (PO2=100 mmHg to <80 mmHg), K+ channels on CB glomus cells are inhibited, causing membrane depolarization to trigger Ca+2 influx and neurotransmitter release that stimulates afferent nerves (1–3). A longstanding model proposes that the CB senses hypoxia through atypical mitochondrial electron transport chain (ETC) metabolism that is more sensitive to decreases in oxygen than other tissues. This model is supported by observations that ETC inhibition by pharmacology and gene knockout activates CB sensory activity and that smaller decreases in oxygen concentration inhibit ETC activity in CB cells compared to other cells (1–5). Determining the composition of atypical ETC subunits in the CB and their specific activities is essential to delineate molecular mechanisms underlying the mitochondrial hypothesis of oxygen sensing. Here, we identify HIGD1C, a novel hypoxia inducible gene domain factor isoform, as an ETC Complex IV (CIV) protein highly and selectively expressed in glomus cells that mediates acute oxygen sensing by the CB. We demonstrate that HIGD1C negatively regulates oxygen consumption by CIV and acts with the hypoxia-induced CIV subunit COX4I2 to enhance the sensitivity of CIV to hypoxia, constituting an important component of mitochondrial oxygen sensing in the CB. Determining how HIGD1C and other atypical CIV proteins expressed in the CB work together to confer exquisite oxygen sensing to the ETC will help us better understand how tissue- and condition-specific CIV subunits contribute to physiological function and disease (6) and allow us to potentially target these proteins to treat chronic diseases characterized by CB dysfunction (7).
Time and spatial trends in landing per unit of effort as support to fisheries management in a multi-gear coastal fishery
Authors: Leitão P. , Sousa L. , Castro M. , Campos A.
Published: October 2021

Landings by the multi-gear coastal fleet operating off the Portuguese continental coast include near 300 species, from which only a few are the object of management plans. In this study, daily landings (kg trip_1) are used, along with an effort indicator, vessel length overall (LoA), to obtain landings per unit of effort (LPUE) as a proxy for the species relative abundance for a total of 48 species. LPUE indices were then used as a response variable in linear models where year (2012-2016), season, region (north and south) and NAO index were included as explanatory variables. Season and region effects were found to significantly affect species abundance for a total of 41 and 40 species respectively, while interannual effects were found to be significant for 19 species, and finally, the NAO index for 3 species. Global LPUE density maps are presented for a number of selected species and a subsample of trips where VMS records were available. For the species analysed, it is proposed that geographic and seasonal changes in LPUE indexes can be used to understand trends in abundance and obtain information that can be used in support of the definition of regional management plans.
Local conjugation of auxin by the GH3 amido synthetases is required for normal development of roots and flowers in Arabidopsis
Authors: Guo Ruipan , Hu Yun , Aoi Yuki , Hira Hayao , Ge Chennan , Dai Xinhua , Kasahara Hiro , Zhao Yunde
Published: October 2021

Gretchen Hagen 3 (GH3) amido synthetases conjugate amino acids to a carboxyl group of small molecules including hormones auxin, jasmonate, and salicylic acid. The Arabidopsis genome harbors 19 GH3 genes, whose exact roles in plant development have been difficult to define because of genetic redundancy among the GH3 genes. Here we use CRISPR/Cas9 gene editing technology to delete the Arabidopsis group II GH3 genes, which are able to conjugate indole-3-acetic acid (IAA) to amino acids. We show that plants lacking the eight group II GH3 genes (gh3 octuple mutants) accumulate free IAA and fail to produce IAA-Asp and IAA-Glu conjugates. Consequently, gh3 octuple mutants have extremely short roots, long and dense root hairs, and long hypocotyls and petioles. Our characterization of gh3 septuple mutants, which provide sensitized backgrounds, reveals that GH3.17 and GH3.9 play prominent roles in root elongation and seed production, respectively. We show that GH3 functions correlate with their expression patterns, suggesting that local deactivation of auxin also contributes to maintaining auxin homeostasis and is important for plant development. Moreover, this work provides a method for elucidating functions of individual members of a gene family, whose members have overlapping functions.
Synthesis, crystal structure and Hirshfeld surface analysis of (4-methylphenyl)[1-(pentafluorophenyl)-5-(trifluoromethyl)-1H-1,2,3-triazol-4-yl]methanone
Authors: Pokhodylo Nazariy T. , Slyvka Yurii , Goreshnik Evgeny , Lytvyn Roman
Published: October 2021

The title compound, C17H7F8N3O, was obtained via the reaction of 1-azido-2,3,4,5,6-pentafluorobenzene with 4,4,4-trifluoro-1-(p-tolyl)butane-1,3-dione using triethylamine as a base catalyst and solvent. The dihedral angles between the pentafluorophenyl (A), triazole (B) and p-tolyl (C) rings are A/B = 62.3 (2), B/C = 43.9 (3) and A/C = 19.1 (3)°. In the crystal, the molecules are linked by C—H...F and C—H...O hydrogen bonds as well as by aromatic π–π stacking interactions into a three-dimensional network. To further analyse the intermolecular interactions, a Hirshfeld surface analysis was performed.
trans-Bis[8-(benzylsulfanyl)quinoline-κ2
N,S]dichloridocobalt(II)
Authors: Kodama Shintaro , Bunno Kazuki , Nomoto Akihiro , Ogawa Akiya
Published: October 2021

The title dichlorocobalt(II) complex, trans-[CoCl2(1)2] [1 = 8-(benzylsulfanyl)quinoline, C16H13NS], has a central CoII atom (site symmetry \overline1) that exhibits a distorted octahedral coordination geometry and is coordinated by two N and two S atoms from the bidentate N,S-ligand (1) situated in an equatorial plane and two Cl atoms in the axial positions. Complexes are linked by weak intermolecular C—H...π interactions between the 8-(benzylsulfanyl)quinoline ligands, forming a chain extending along the a-axis direction.
Links, fit or sacrifice: job embeddedness and intention to quit among Generation Y
Authors: Fuchs Rosa María
Published: October 2021

Purpose

The study aims to determine how the relationship among links, fit and sacrifice (dimensions of job embeddedness) influence employees' intention to quit in the case of professionals belonging to Generation Y.

Design/methodology/approach

A quantitative correlational study was conducted with a cross-sectional dimension of time. The survey technique was applied through a certified online panel. The sample consisted of 211 members of Generation Y.

Findings

It has been verified that the only significant dimension for Generation Y is sacrifice.

Research limitations/implications

It is necessary to extend the study of the dimensions of job embeddedness and their influence on employees' intention to quit in different demographic groups. It would be advisable to conduct longitudinal studies to observe the dynamics of job embeddedness throughout the years.

Practical implications

Organizations concerned with retaining the talent of young professionals can focus on the development of policies and benefits that encourage sacrifice.

Social implications

The finding that the sacrifice dimension is the one that would reduce the intention to leave for Generation Y will help to ensure that organizations retain the workforce that they value.

Originality/value

The study is important to gain a better understanding of Generation Y behavior. In addition, in response to the demand from the literature, the sample considered only Generation Y with work experience.
Motivational determinants of digital ticketing: the mediating effect of service satisfaction and the moderating effect of psychological discomfort
Authors: Kim Sanghoon , Yu Ho Yeol , Lee Hyun-Woo
Published: October 2021

Purpose

The purpose of the study was (1) to examine the motivational composites determining consumers' continued intention to use digital ticketing via self-service technology (SST) by integrating service satisfaction and (2) to ascertain the differences between consumers according to their psychological discomfort toward technology.

Design/methodology/approach

Data were collected using a structured questionnaire, and a total of 323 were included in the analysis. Partial least squares structural equation modeling (PLS-SEM) was utilized to test motivational determinants of digital ticketing. In addition, permutation-based multi-group analysis was performed to investigate the differences between consumers with high and low technology discomfort.

Findings

Both intrinsic and extrinsic motivation are positive predictors of continued intention to use digital ticketing, but only intrinsic motivation has a positive impact on continued intention through service satisfaction. Moreover, the relationship between intrinsic motivation, service satisfaction and continued intention was stronger for consumers with high psychological discomfort than those with low psychological discomfort.

Originality/value

Given the conspicuous characteristics of the digital ticketing process for sporting events, the insights gained from the study may be of assistance to researchers and practitioners in understanding sport consumers' ticket consumption behavior and the determinants of SST usage.
International STEM pre-service teachers’ intercultural competence
Authors: Galamba Arthur
Published: October 2021

Purpose

The author is interested in how international (migrant) pre-service teachers use their educational background knowledge and worldviews to make sense of the educational system, the pedagogy and of power relations between staff members in the hosting country. The author seeks to unveil their understanding of successful intellectual integration and their strategies to navigate social, conceptual and pedagogical obstacles.

Design/methodology/approach

The author draws on the concept of “intercultural competence” to analyse how international STEM pre-service teachers respond to the challenges and opportunities of integration in the English system. A total of 18 participants were interviewed in focus groups in London to find out about their perceptions of the course and attitudes during their training journey. Five hours of audio recording were transcribed and a thematic analysis was carried out.

Findings

International STEM pre-service teachers experience challenges to intellectual integration, including understanding the new school culture, school structure, teaching methodologies and the use of specialist terminologies. However, they show little concern about networking and relations of power.

Practical implications

Mentors and tutors should not assume school systems are the same everywhere. Support from university tutors and school mentors must take into consideration that international students will very likely hold ethnocentric views. Mentors, tutors and pre-service teachers would benefit very much from bespoke support to help international students to integrate in a new educational system.

Originality/value

Very little has been reported on the experience of international STEM pre-service teachers in England, particularly those with no previous teaching experience. The objective of this study is to address this gap and contribute to the internationalisation of teacher training curricula.
Relationships between policy, teachers' values and professional capital in teacher collaboration in hierarchical Chinese societies
Authors: Lee Daphnee Hui Lin
Published: October 2021

Purpose

Both Hong Kong and Singapore leverage teacher collaboration to improve student learning, but state reforms differ in how teacher collaborative capabilities are prioritized. This paper provides a nuanced comparison of Hong Kong and Singapore teachers' values (risk-taking, power distance and uncertainty avoidance) to develop insights into how different policy focuses cultivate teachers' capabilities to focus on improving student learning.

Design/methodology/approach

Employing Hargreaves and Fullan's (2012) concept of professional capital, statistical analyses determine teachers' values profiles of high, medium and low professional capital in the respective contexts. Leveraging related research on Singapore teachers (Lee and Lee, 2018), nuances in teachers' values in the Hong Kong results are identified via cluster analysis and explained via structural equation modelling.

Findings

Medium professional capital Hong Kong teachers' values matched Singapore's, but teachers in other clusters are nuanced. Compared to Singapore teachers with similar levels of professional capital, high professional capital Hong Kong teachers have higher uncertainty avoidance, while low professional capital teachers are the opposite. In Hong Kong, high uncertainty avoidance values positively influence teacher leadership and focus on student learning. Nevertheless, as with their Singapore counterparts, high professional capital Hong Kong teachers have low power distance and high risk-taking values.

Originality/value

This paper raises awareness regarding policy's influence in cultivating teachers' values and their transformational change capabilities. By comparing two hierarchical Chinese societies, the discussion questions whether Chinese and Western cultural influences are mutually exclusive, and whether transformational change in cultural values, if achievable, is necessary.
Port's technologies for autonomous ships in restricted waters
Authors: Sinohara Helio Takahiro , Tannuri Eduardo Aoun
Published: October 2021

Purpose

This work analyses autonomous ships' specific needs of external and environmental information in restricted pilotage waters. Harbour pilots use conventional well-tested techniques when piloting the manned vessel. In this work, the authors propose technological solutions to be installed or adapted in ports to feed the autonomous ships' systems with the information considered relevant by pilots.

Design/methodology/approach

To investigate what pilots consider relevant, the authors submitted a questionnaire to the pilotage of Paranaguá Port. Then the authors presented a case study including the critical areas for the navigation of ships.

Findings

These technological solutions aim to allow vessels reaching critical areas in a position, a time, a speed and a course that compensates the external forces and/or avoid high-risk situations. The authors have proposed technological solutions considering those already available in the ports, particularly in Paranaguá and Antonina in Brazil.

Originality/value

There is little published data on navigation of ships in pilotage waters. So far, there has been little discussion on autonomous ships in restricted waters.
Exploring enablers of modularity in healthcare service delivery
Authors: Prakash Gyan
Published: October 2021

Purpose

This paper explores the enablers of modular healthcare services.

Design/methodology/approach

A survey-based approach was adopted with specialised hospitals as the unit of analysis. A structural model was developed based on a literature review and assessed using a cross-sectional research design. A 23-indicator questionnaire was circulated among service providers in the healthcare system across India, and 286 valid responses were received. The data were analysed using partial least squares-structural equation modeling (PLS-SEM).

Findings

The results reveal that professional competence, technological versatility, clear division of tasks, channelised flow of information and professional autonomy act as enablers that may drive modular service delivery.

Research limitations/implications

By examining service providers' perspectives, this paper highlights the influence of the identified enablers on modular service delivery in healthcare organisations.

Practical implications

For practitioners, the study provides suggestions for designing patient-centric healthcare services via modular healthcare delivery. The identified structural relationships can facilitate immediate corrective actions and the formulation of future policies. The findings will help practitioners foresee opportunities for patient participation in value co-creation, meet patients' varying needs, decompose service offerings, mix and match components develop sets of rules as interfaces between service modules and design service packages on an ongoing basis.

Social implications

This study underscores the emergence of patient-centric care and may aid the design of processes that deliver health to the patient as a person.

Originality/value

This paper identifies and empirically validates relationships between healthcare service delivery processes and modular service delivery.
Nongenetic inheritance of behavioural variability is context specific and sex specific
Authors: Moschilla Joe A. , Tomkins Joseph L. , Simmons Leigh W.
Published: October 2021

Environmentally mediated nongenetic inheritance extends the concept of phenotypic plasticity across generations, allowing for the experience of parents to influence the physiology, life history and behaviour of their offspring.

We assess whether the perceived social environment of mothers and fathers impacts offspring behaviour in the Australian field cricketTeleogryllus oceanicus.

We varied parents' perception of the density of conspecific males by exposing parents to either the presence or absence of male song throughout rearing. Following mating in a factorial design, the offspring of the parental pairs were also reared across the two acoustic environments and their behaviour assessed as adults.

When reared in a no‐song environment, offspring of both sexes were more active, emerging from a shelter sooner and displaying greater mobility in search of male song.

Offspring behaviour was not directly impacted by either the maternal or paternal social environments independently, but there was a significant interaction effect between the parental environments on the behaviour of daughters. When both parents were reared in song (‘paternal song × maternal song’), their no‐song‐reared daughters exhibited lower levels of mobility than the no‐song‐reared daughters of ‘paternal song × maternal no‐song’ and ‘paternal no‐song × maternal song’ pairs.

Although our data suggest that nongenetic parental effects may have the potential to drive behavioural variability in offspring, such effects are highly complex, only arising as sex‐ and context‐specific traits.

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