bluuebunny/crossref_metadata_2025 huggingface dataset:
Real-time clinician text feeds from electronic health records
Authors: Teo James , Dinu Vlad , Bernal William , Davidson Phil , Oliynyk Vitaliy , Breen Cormac , Barker Richard D , Dobson Richard
Published: October 2020

Analyses of search engine and social media feeds have been attempted for infectious disease outbreaks1, but have been found to be susceptible to artefactual distortions from health scares or keyword spamming in social media or the public internet 2–4. We describe an approach using real-time aggregation of keywords and phrases of free text from real-time clinician-generated documentation in electronic health records to produce a customisable real-time viral pneumonia signal providing up to 2 days warning for secondary care capacity planning. This low-cost approach is open-source, is locally customisable, is not dependent on any specific electronic health record system and can be deployed at multiple organisational scales.
Neurogenetic and genomic approaches reveal roles for Dpr/DIP cell adhesion molecules inDrosophilareproductive behavior
Authors: Brovero Savannah G , Fortier Julia C , Hu Hongru , Lovejoy Pamela C , Newell Nicole R , Palmateer Colleen M , Tzeng Ruei-Ying , Lee Pei-Tseng , Zinn Kai , Arbeitman Michelle N
Published: October 2020

Drosophilareproductive behaviors are directed byfruitlessneurons (fru P1isoforms). A reanalysis of genomic studies shows that genes encodingdprandDIPImmunoglobulin superfamily (IgSF) members are expressed infru P1neurons. Eachfru P1anddpr/DIP(fru P1∩dpr/DIP) overlapping expression pattern is similar in both sexes, with dimorphism in neuronal morphology and cell number. Behavioral studies offru P1∩dpr/DIPperturbation genotypes point to the mushroom body functioning together with the lateral protocerebral complex. Functionally, we find that perturbations of sex hierarchy genes andDIP-εchanges sex-specific morphology offru P1∩DIP-αneurons. A single-cell RNA-seq analysis shows that theDIPshave high expression in a restricted set offru P1neurons, whereas thedprsare expressed in larger set of neurons at intermediate levels, with a myriad of combinations.
Vascular origins of low-frequency oscillations in the cerebrospinal fluid signal in resting-state fMRI: Interpretation using photoplethysmography
Authors: Attarpour Ahmadreza , Ward James , Chen J. Jean
Published: October 2020

Slow and rhythmic spontaneous oscillations of cerebral blood flow are well known to have diagnostic utility, notably frequencies of 0.008-0.03 Hz (B-waves) and 0.05-0.15Hz (Mayer waves or M waves). However, intracranial measurements of these oscillations have been difficult. Oscillations in the cerebrospinal fluid (CSF), which are influenced by the cardiac pulse wave, represent a possible avenue for non-invasively tracking these oscillations using resting-state functional MRI (rs-fMRI), and have been used to correct for vascular oscillations in rs-fMRI functional connectivity calculations. However, the relationship between low-frequency CSF and vascular oscillations is unclear. In this study, we investigate this relationship using fast simultaneous multi-slice rs-fMRI coupled with fingertip photoplethysmography (PPG). We not only extract B-wave and M-wave range spectral power from the PPG signal, but also derive the pulse-intensity ratio (PIR, a surrogate of slow blood-pressure oscillations), the second-derivative of the PPG (SDPPG, a surrogate of arterial stiffness) and heart-rate variability (HRV). The main findings of this study are: (1) signals in different CSF regions (ROIs) are not equivalent in their vascular contributions or in their associations with vascular and tissue rs-fMRI signals; (2) the PPG signal contains the highest signal contribution from the M-wave range, while PIR contains the highest signal contribution from the B-wave range; (3) in the low-frequency range, PIR is more strongly associated with rs-fMRI signal in the CSF than PPG itself, and than HRV and SDPPG; (4) PPG-related vascular oscillations only contribute to < 20% of the CSF signal in rs-fMRI, insufficient support for the assumption that low-frequency CSF signal fluctuations directly reflect vascular oscillations. These findings caution the use of CSF as a monolithic region for extracting physiological nuisance regressors in rs-fMRI applications. They also pave the way for using rs-fMRI in the CSF as a potential tool for tracking cerebrovascular health through, for instance the strong relationship between PIR and the CSF signal.
Adhesion to type I collagen fibrous gels induces E- to N-cadherin switching without other EMT-related phenotypes in lung carcinoma cell A549
Authors: Fujisaki Hitomi , Futaki Sugiko , Yamada Masashi , Sekiguchi Kiyotoshi , Hayashi Toshihiko , Hattori Shunji
Published: October 2020

In culture system, environmental factors, such as increasing exogenous growth factors and adhesion to type I collagen (Col-I) induce epithelial-to-mesenchymal transition (EMT) in cells. Col-I molecules maintain a non-fibril form under acidic conditions, and they reassemble into fibrils under physiological conditions. Col-I fibrils often assemble to form three-dimensional gels. The gels and non-gel-form of Col-I can be utilized as culture substrates and different gel-forming state often elicit different cell behaviors. However, gel-form dependent effects on cell behaviors, including EMT induction, remain unclear. EMT induction in lung cancer cell line A549 has been reported via adhesion to Col-I but the effects of gel form dependency are unelucidated. This study investigated the changes in EMT-related behaviors in A549 cells cultured on Col-I gels.

We examined cell morphology, proliferation, single-cell migration and expression of EMT-related features in A549 cells cultured on gels or non-gel form of Col-I and non-treated dish with or without transforming growth factor (TGF)-β1. On Col-I gels, some cells kept cell–cell contacts and formed clusters, others maintained single-cell form. In cell–cell contact regions, E-cadherin expression was downregulated, whereas that of N-cadherin was upregulated. Vimentin and integrins α2 and β1 expression were not increased. In TGF-β1-treated A549 cells, cadherin switched from E- to N-cadherin. Their morphology changed to a mesenchymal form and cells scattered with no cluster formation. Vimentin, integrins α2 and β1 expression were upregulated. Thus, we concluded that culture on Col-I fibrous gels induced E- to N-cadherin switching without other EMT-related phenotypes in A549 cells.
Diversity and asynchrony in soil microbial communities stabilizes ecosystem functioning
Authors: Wagg Cameron , Hautier Yann , Pellkofer Sarah , Banerjee Samiran , Schmid Bernhard , van der Heijden Marcel G.A.
Published: October 2020

Theoretical and empirical advances have revealed the importance of biodiversity for stabilizing ecosystem functions through time. Yet despite the global degradation of soils, how the loss of soil microbial diversity can de-stabilizes ecosystem functioning is unknown. Here we experimentally quantified the contribution diversity and the temporal dynamics in the composition of soil microbial communities to the temporal stability of four key ecosystem functions related to nutrient and carbon cycling. Soil microbial diversity loss reduced the temporal stability of all ecosystem functions and was particularly strong when over 50% of microbial taxa were lost. The stabilizing effect of soil biodiversity was linked to asynchrony among microbial taxa whereby different soil fungi and bacteria were associated with different ecosystem functions at different times. Our results emphasize the need to conserve soil biodiversity in order to ensure the reliable provisioning of multiple ecosystems functions that soils provide to society.
Malignant astrocyte swelling and impaired glutamate clearance drive the expansion of injurious spreading depolarization foci
Authors: Menyhárt Ákos , Frank Rita , Farkas Attila E. , Süle Zoltán , Varga Viktória É. , Nyúl-Tóth Ádám , Meiller Anne , Ivánkovits-Kiss Orsolya , Lemale Coline L. , Szabó Írisz , Tóth Réka , Zölei-Szénási Dániel , Woitzik Johannes , Marinesco Stephane , Krizbai István A. , Bari Ferenc , Dreier Jens P. , Farkas Eszter
Published: October 2020

Spreading depolarizations (SD) indicate infarct maturation and predict worse clinical outcome in ischemic stroke. We demonstrate here in rodents that brain edema formation upon ischemic stroke impairs astroglial glutamate clearance and increases the tissue area invaded by SD. The cytotoxic glutamate accumulation predisposes an extensive bulk of tissue for a yet undescribed simultaneous depolarization (SiD). We confirm in rat brain slices under hypo-osmotic stress that SiD is the pathological expansion of prior SD foci, is associated with astrocyte swelling and triggers oncotic neuron death. The blockade of astrocytic aquaporin-4 channels and Na+/K+/Cl-co-transporters, or volume-regulated anion channels mitigated slice edema, glutamate accumulation and SiD occurrence. Reversal of slice edema by hyperosmotic treatment counteracted glutamate accumulation and prevented SiD. In contrast, paralysis of astrocyte metabolism or inhibition of astrocyte glutamate uptake reproduced the SiD phenotype. We discuss our results in the light of evidence for SiD in the human cortex. Our results emphasize the need of preventive osmotherapy in ischemic stroke.
Genetic mapping of the early responses to salt stress inArabidopsis thaliana
Authors: Awlia Mariam , Alshareef Nouf , Saber Noha , Korte Arthur , Oakey Helena , Panzarová Klára , Trtílek Martin , Negrão Sónia , Tester Mark , Julkowska Magdalena M.
Published: October 2020

Salt stress decreases plant growth prior to significant ion accumulation in the shoot. However, the processes underlying this rapid reduction in growth are still unknown. To understand the changes in salt stress responses through time and at multiple physiological levels, examining different plant processes within a single setup is required. Recent advances in phenotyping has allowed the image-based estimation of plant growth, morphology, colour and photosynthetic activity. In this study, we examined the salt stress-induced responses of 191 Arabidopsis accessions from one hour to seven days after treatment using high-throughput phenotyping. Multivariate analyses and machine learning algorithms identified that quantum yield measured in the light-adapted state (Fv′/Fm′) greatly affected growth maintenance in the early phase of salt stress, while maximum quantum yield (QY max) was crucial at a later stage. In addition, our genome-wide association study (GWAS) identified 770 loci that were specific to salt stress, in which two loci associated with QY max and Fv′/Fm′ were selected for validation using T-DNA insertion lines. We characterised an unknown protein kinase found in the QY max locus, which reduced photosynthetic efficiency and growth maintenance under salt stress. Understanding the molecular context of the identified candidate genes will provide valuable insights into the early plant responses to salt stress. Furthermore, our work incorporates high-throughput phenotyping, multivariate analyses and GWAS, uncovering details of temporal stress responses, while identifying associations across different traits and time points, which likely constitute the genetic components of salinity tolerance.
Glucose-lactose mixture feeds in industry-like conditions: a gene regulatory network analysis on the hyperproducingTrichoderma reeseistrain Rut-C30
Authors: Pirayre Aurélie , Duval Laurent , Blugeon Corinne , Firmo Cyril , Perrin Sandrine , Jourdier Etienne , Margeot Antoine , Bidard Frédérique
Published: October 2020

Background

The degradation of cellulose and hemicellulose molecules into simpler sugars such as glucose is part of the second generation biofuel production process. Hydrolysis of lignocellulosic substrates is usually performed by enzymes produced and secreted by the fungusTrichoderma reesei. Studies identifying transcription factors involved in the regulation of cellulase production have been conducted but no overview of the whole regulation network is available. A transcriptomic approach with mixtures of glucose and lactose, used as a substrate for cellulase induction, was used to help us decipher missing parts in the network.

Results

Experimental results confirmed the impact of sugar mixture on the enzymatic cocktail composition. The transcriptomic study shows a temporal regulation of the main transcription factors and a lactose concentration impact on the transcriptional profile. A gene regulatory network (GRN) built using the BRANE Cut software reveals three sub-networks related toia positive correlation between lactose concentration and cellulase production,iia particular dependence of the lactose onto theβ-glucosidase regulation andiiia negative regulation of the development process and growth.

Conclusions

This work is the first investigating a transcriptomic study regarding the effects of pure and mixed carbon sources in a fed-batch mode. Our study expose a co-orchestration ofxyr1,clr2andace3for cellulase and hemicellulase induction and production, a fine regulation of theβ-glucosidase and a decrease of growth in favor of cellulase production. These conclusions provide us with potential targets for further genetic engineering leading to better cellulase-producing strains.
Niche evolution of the Neotropical tree genusOtobain the context of global biogeography of the nutmeg family, Myristicaceae
Authors: Frost Laura , Santamaría-Aguilar Daniel A. , Singletary Daisy , Lagomarsino Laura P.
Published: October 2020

Aim

Plant distributions are influenced by species’ ability to colonize new areas via long-distance dispersal and propensity to adapt to new environments via niche evolution. We useOtoba(Myristicaceae), an ecologically dominant tree genus found in low-to-mid elevation wet forests, as a system to understand the relative importance of these processes within the Neotropics, a region characterized by high species richness and a diversity of biomes.

Location

Neotropics and global

Taxon

Otobaand entire Myristicaceae

Methods

We resolve the first phylogeny ofOtobausing targeted sequence capture phylogenomics. We pair this with the most densely sampled phylogeny of Myristicaceae to date, inferred using publicly available data. We then use phylogenetic comparative methods to infer biogeography and examine patterns of niche evolution.

Results

Myristicaceae has an Old World origin, with a single expansion event into the Americas. Divergence dates, fossil evidence, and a notable lack of long-distance dispersal are consistent with a Boreotropical origin of Neotropical Myristicaceae. Mirroring the rarity of dispersal at the family level,Otoba’s biogeography is marked by few biogeographic events: two expansions into Central America from a South American ancestor and a single dispersal event across the Andes. This limited movement contrasts with rapid climatic niche evolution, typically occurring across geographically proximate habitats.

Main conclusions

Contrasting with previous studies, long-distance dispersal does not need to be invoked to explain the pantropical distribution of Myristicaceae, nor the biogeography ofOtoba. This likely results from the family’s relatively large seeds that are dispersed by large-bodied vertebrates. Instead, rapid niche evolution inOtobahas facilitated its occurrence throughout mesic habitats of the northern Neotropics, including the Amazon rainforest and Andean montane forests.Otobaadds to a growing group of Neotropical plant clades in which climate adaptation following local migration is common, implying an important role of niche evolution in the assembly of the Neotropical flora.

Significance statement

Species distributions across the climatically and topographically heterogenous Neotropics are explained by a combination of local adaptation and dispersal. The relative importance of these mechanisms is clade dependent. We find that niche evolution in geographically proximal habitats is much more common than long-distance dispersal to preadapted regions in the tree genusOtoba, which includes both hyperdominant Amazonian species and narrow Andean endemics. The lack of long-distance dispersal is likely due toOtoba’s large seeds. Our results add to a growing body of literature demonstrating a key role of labile niche evolution across steep environmental gradients in Neotropical plant biogeography.
Modulation of early host innate immune response by a Fowlpox virus (FWPV) lateral body protein
Authors: Giotis Efstathios S , Laidlaw Stephen M , Bidgood Susanna R , Albrecht David , Burden Jemima J , Robey Rebecca C , Mercer Jason , Skinner Michael A
Published: October 2020

The avian pathogen, fowlpox virus (FWPV) has been successfully used as vaccine vector in poultry and humans but relatively little is known about its ability to modulate host antiviral immune responses in these hosts, which are replication permissive and non-permissive, respectively. FWPV is highly resistant to avian type I interferon (IFN) and able to completely block the host IFN-response. Microarray screening of host IFN-regulated gene expression in cells infected with 59 different, non-essential FWPV gene knock-out mutants revealed that FPV184 confers immunomodulatory capacity. We report thatFPV184-knockout virus (FWPVΔ184) induces the cellular IFN response as early as 2 hours post-infection. The wild-type, uninduced phenotype can be rescued by transient expression ofFPV184in FWPVΔ184-infected cells. Ectopic expression ofFPV184inhibited polyI:C activation of the chicken IFN-β promoter and IFN-α activation of the chicken Mx promoter. Confocal and correlative super-resolution light and electron microscopy demonstrated that FPV184 has a functional nuclear localisation signal domain and is packaged in the lateral bodies of the virions. Taken together, these results provide a paradigm for a late poxvirus structural protein packaged in the lateral bodies and capable of supressing IFN induction early during the next round of infection.
On-tissue spatially-resolved glycoproteomics guided by N-glycan imaging reveal global dysregulation of canine glioma glycoproteomic landscape
Authors: Malaker Stacy A. , Quanico Jusal , Romero Antonella Raffo , Kobeissy Firas , Aboulouard Soulaimane , Tierny Dominique , Bertozzi Carolyn R. , Fournier Isabelle , Salzet Michel
Published: October 2020

Here we present an approach to identify N-linked glycoproteins and deduce their spatial localization using a combination of MALDI mass spectrometry N-glycan imaging and spatially-resolved glycoproteomic strategies. We subjected formalin-fixed, paraffin-embedded glioma biopsies to on-tissue PNGaseF digestion and MALDI imaging and found that the glycan HexNAc4-Hex5-NeuAc2 was found to be predominantly expressed in necrotic regions of high-grade canine gliomas, whereas high mannose HexNAc2-Hex5 was predominantly found in benign regions. To determine the underlying sialo-glycoprotein, various regions in adjacent tissue sections were subjected to microdigestion and the extracts were analyzed by LC-MS/MS without further glycopeptide enrichment. Results identified haptoglobin, which is involved in iron scavenging that presents aberrant fucosylation/sialylation in various cancers, as the protein associated with HexNAc4-Hex5-NeuAc2. Additionally, we identified several high-mannose (Hex2-HexNAc5) glycopeptides enriched in benign regions. To the best of our knowledge, this is the first report that directly links glycan imaging with intact glycopeptide identification. In total, our spatially-resolved glycoproteomics technique identified over 400 N-glycosylated, O-GalNAcylated, O-mannosylated, and S- and O-GlcNAcylated glycopeptides from over 30 proteins, demonstrating the diverse array of glycosylation present on the tissue slides and the sensitivity of our technique. While N-glycosylation and O-mannosylation were similar between benign and tumor/necrotic sections, S- and O-GlcNAc glycopeptides were significantly deceased in tumor/necrotic sections, whereas sialylated O-GalNAc glycopeptides were significantly upregulated. Ultimately, this proof-of-principle work demonstrates the capability of spatially-resolved glycoproteomics to complement MALDI-imaging technologies in understanding dysregulated glycosylation in cancer.
Antibody-drug conjugates targeting CD45 plus Janus kinase inhibitors effectively condition for allogeneic hematopoietic stem cell transplantation
Authors: Persaud Stephen P. , Ritchey Julie K. , Choi Jaebok , Ruminski Peter G. , Cooper Matthew L. , Rettig Michael P. , DiPersio John F.
Published: October 2020

Despite the curative potential of hematopoietic stem cell transplantation (HSCT), transplant conditioning-associated toxicities preclude broader clinical application. Antibody-drug conjugates (ADC) provide an attractive approach to HSCT conditioning that minimizes toxicity while retaining efficacy. Initial studies of ADC conditioning have largely involved syngeneic HSCT; however, for treatment of acute leukemias or tolerance induction for solid organ transplantation, strategies for allogeneic HSCT (allo-HSCT) are needed. Using murine allo-HSCT models, we show that combining CD45-targeted ADCs with the Janus kinase inhibitor baricitinib enables multilineage alloengraftment with >80-90% donor chimerism. Mechanistically, baricitinib impaired T and NK cell survival, proliferation and effector function, with NK cells being particularly susceptible due to inhibited IL-15 signaling. Unlike irradiated mice, CD45-ADC-conditioned mice did not manifest graft-versus-host alloreactivity when challenged with mismatched T cells. Our studies demonstrate novel allo-HSCT conditioning strategies that exemplify the promise of immunotherapy to improve the safe application of HSCT for treating hematologic diseases.
Projection in genomic analysis: A theoretical basis to rationalize tensor decomposition and principal component analysis as feature selection tools
Authors: Taguchi Y-h. , Turki Turki
Published: October 2020

Identifying differentially expressed genes is difficult because of the small number of available samples compared with the large number of genes. Conventional gene selection methods employing statistical tests have the critical problem of heavy dependence ofP-values on sample size. Although the recently proposed principal component analysis (PCA) and tensor decomposition (TD)-based unsupervised feature extraction (FE) has often outperformed these statistical test-based methods, the reason why they worked so well is unclear. In this study, we aim to understand this reason in the context of projection pursuit (PP) that was proposed a long time ago to solve the problem of dimensions; we can relate the space spanned by singular value vectors with that spanned by the optimal cluster centroids obtained from K-means. Thus, the success of PCA- and TD-based unsupervised FE can be understood by this equivalence. In addition to this, empirical threshold adjustedP-values of 0.01 assuming the null hypothesis that singular value vectors attributed to genes obey the Gaussian distribution empirically corresponds to threshold-adjustedP-values of 0.1 when the null distribution is generated by gene order shuffling. For this purpose, we newly applied PP to the three data sets to which PCA and TD based unsupervised FE were previously applied; these data sets treated two topics, biomarker identification for kidney cancers (the first two) and the drug discovery for COVID-19 (the thrid one). Then we found the coincidence between PP and PCA or TD based unsupervised FE is pretty well. Shuffling procedures described above are also successfully applied to these three data sets. These findings thus rationalize the success of PCA- and TD-based unsupervised FE for the first time.
Intracellular label-free detection of mesenchymal stem cell metabolism within a perivascular niche-on-a-chip
Authors: Perottoni Simone , Neto Nuno G. B. , Di Nitto Cesare , Raimondi Manuela Teresa , Monaghan Michael G.
Published: October 2020

The stem cell niche at the perivascular space in human tissue plays a pivotal role in dictating the overall fate of stem cells within it. Mesenchymal stem cells (MSCs), in particular, experience influential microenvironmental conditions, which induce specific metabolic profiles that affect processes such as cell differentiation and dysregulation of the immunomodulatory funtion. Reports focusing specifically on the metabolic status of MSCs under the effect of pathophysiological stimuli - in terms of flow velocities, shear stresses or oxygen tension – do not model heterogenous gradients, highlighting the need of more advanced models reproducing the metabolic niche. Organ-on-a-chip technology offers the most advanced tools for stem cell niche modelling thus allowing for controlled dynamic culture conditions while profiling tunable oxygen tension gradients. However, current systems for live cell detection of metabolic activity inside microfluidic devices require the integration of microsensors that allow for extracellular measurments only, giving innacurate and indirect information about the metabolic state of cells. Here, we present a metabolic toolbox coupling a miniatuirzedin vitrosystem for human-MSCs dynamic culture, that mimics microenvironmental conditions of the perivascular niche, with high-resolution imaging of intracellular metabolism. Using Fluorescence Lifetime Imaging Microscopy (FLIM) we monitor the spatial metabolic machinery and correlate it with experimentally validated intracellular oxygen concentration after designing the oxygen tension decay along the fluidic chamber byin silicomodels prediction. Our platform allows for the subjection of a metabolic profile to MSCs, mimicking the physiological niche in space and time, and its real-time monitoring representing a functional tool for modelling perivascular niches, relevant diseases and metabolic-related uptake of pharmaceuticals.
The mTORC1-mediated activation of ATF4 promotes protein and glutathione synthesis downstream of growth signals
Authors: Torrence Margaret E. , MacArthur Michael R. , Hosios Aaron M. , Valvezan Alexander J. , Asara John M. , Mitchell James R. , Manning Brendan D.
Published: October 2020

The mechanistic target of rapamycin complex 1 (mTORC1) stimulates a coordinated anabolic program in response to growth-promoting signals. Paradoxically, recent studies indicate that mTORC1 can activate the adaptive stress-responsive transcription factor ATF4 through mechanisms distinct from its canonical induction by the integrated stress response (ISR). However, how ATF4 functions in response to these distinct modes of regulation and its broader role as a downstream target of mTORC1 are unknown. Therefore, we directly compared ATF4-dependent transcriptional changes induced upon activation of mTORC1 or the ISR. The mTORC1-ATF4 pathway stimulated the expression of only a subset of the ATF4 target genes stimulated by the ISR, including genes involved in amino acid uptake, synthesis, and tRNA charging. We demonstrate that ATF4 is a metabolic effector of mTORC1 involved in both its established role in promoting protein synthesis and in a previously unappreciated function for mTORC1 in stimulating cellular cystine uptake and glutathione synthesis.
Sedimentation rate and organic matter dynamics shape microbiomes across a continental margin
Authors: Bhattacharya Sabyasachi , Mapder Tarunendu , Fernandes Svetlana , Roy Chayan , Sarkar Jagannath , Rameez Moidu Jameela , Mandal Subhrangshu , Sar Abhijit , Chakraborty Amit Kumar , Mondal Nibendu , Dam Bomba , Peketi Aditya , Chakraborty Ranadhir , Mazumdar Aninda , Ghosh Wriddhiman
Published: October 2020

Marine sedimentation rate and bottom-water O2concentration control the remineralization/sequestration of organic carbon across continental margins; but whether/how they shape microbiome architecture (the ultimate effector of all biogeochemical phenomena), across shelf/slope sediments, is unknown. Here we reveal distinct microbiome structures and functions, amidst comparable pore-fluid chemistries, along ~3 m sediment-horizons underlying the seasonal (shallow coastal) and perennial (deep sea) oxygen minimum zones (OMZs) of the Arabian Sea, situated across the western-Indian margin (water-depths: 31 m and, 530 and 580 m, respectively). Along the perennial- and seasonal-OMZ sediment-cores microbial communities were predominated byGammaproteobacteria/AlphaproteobacteriaandEuryarchaeota/Firmicutesrespectively. As a perennial-OMZ signature, a cryptic methane production-consumption cycle was found to operate near the sediment-surface; overall diversity, as well as the relative abundances of simple-fatty-acids-requiring anaerobes (methanogens, anaerobic methane-oxidizers, sulfate-reducers and acetogens), peaked in the topmost sediment-layer and then declined via synchronized fluctuations until the sulfate-methane transition zone was reached. The entire microbiome profile was reverse in the seasonal-OMZ sediment-horizon. We discerned that in the perennial-OMZ sediments organic carbon deposited was higher in concentration, and marine components-rich, so it potentially degraded readily to simple fatty acids; lower sedimentation rate afforded higher O2exposure time for organic matter degradation despite perennial hypoxia in the bottom-water; thus, the resultant abundance of reduced metabolites sustained multiple inter-competing microbial processes in the upper sediment-layers. Remarkably, the whole geomicrobial scenario was opposite in the sediments of the seasonal/shallow-water OMZ. Our findings create a microbiological baseline for understanding carbon-sulfur cycling across distinct marine depositional settings and water-colum n oxygenation regimes.
Fitness Estimation for Genetic Evolution of Bacterial Populations
Authors: Sarkisov Sergey S. , Timofeyev Ilya , Azencott Robert
Published: October 2020

In this paper we develop and test algorithmic techniques to estimate genotypes fitnesses by analysis of observed daily frequency data monitoring the long-term evolution of bacterial populations. In particular, we develop a non-linear least squares approach to estimate selective advantages of emerging new mutant strains in locked-box stochastic models describing bacterial genetic evolution similar to the celebrated Lenski experiment on Escherichia Coli. Our algorithm first analyses emergence of new mutant strains for each individual trajectory. For each trajectory our analysis is progressive in time, and successively focuses on the first mutation event before analyzing the second mutation event. The basic principle applied here is to minimize (for each trajectory) the mean squared errors of predictionw(t) −W(t) where the observed white cell frequenciesw(t) are predicted byW(t), which is computed as the conditional expectation ofw(t) given the available information at time (t− 1). The pooling of all selective advantages estimates across all trajectories provides histograms on which we perform a precise peak analysis to compute final estimates of selective advantages. We validate our approach using ensembles of simulated trajectories.
Plectin Ensures Intestinal Epithelial Integrity and Protects Colon Against Colitis
Authors: Krausova Alzbeta , Buresova Petra , Sarnova Lenka , Oyman-Eyrilmez Gizem , Skarda Jozef , Wohl Pavel , Bajer Lukas , Sticova Eva , Bartonova Lenka , Pacha Jiri , Koubkova Gizela , Prochazka Jan , Spörrer Marina , Dürrbeck Christopher , Stehlikova Zuzana , Vit Martin , Ziolkowska Natalia , Sedlacek Radislav , Jirak Daniel , Kverka Miloslav , Wiche Gerhard , Fabry Ben , Korinek Vladimir , Gregor Martin
Published: October 2020

Plectin, a highly versatile cytolinker protein, provides tissues with mechanical stability through the integration of intermediate filaments (IFs) with cell junctions. Here, we hypothesize that plectin-controlled cytoarchitecture is a critical determinant of the intestinal barrier function and homeostasis. Mice lacking plectin in intestinal epithelial cells (IEC;PleΔIEC) spontaneously developed colitis characterized by extensive detachment of IECs from the basement membrane (BM), increased intestinal permeability, and inflammatory lesions. Moreover, plectin expression was reduced in colons of ulcerative colitis (UC) patients and negatively correlated with the severity of colitis. Mechanistically, plectin deficiency in IECs led to aberrant keratin filament (KF) network organization and formation of dysfunctional hemidesmosomes (HDs) and intercellular junctions. In addition, the hemidesmosomal α6β4 integrin (Itg) receptor showed attenuated association with KFs, and protein profiling revealed prominent downregulation of junctional constituents. Consistent with effects of plectin loss in the intestinal epithelium, plectin-deficient IECs exhibited remarkably reduced mechanical stability and limited adhesion capacityin vitro. Feeding mice with a low-residue liquid diet that reduced mechanical stress and antibiotic treatment successfully mitigated epithelial damage in thePleΔIECcolon.
Hybrid organizations and an ethic of accountability: the role of accountability systems in constructing responsible hybridity
Authors: Baudot Lisa , Dillard Jesse , Pencle Nadra
Published: October 2020

Purpose

Building on the research program of Dillard and Brown (2015) and Dillard and Vinnari (2019), specifically related to an “ethic of accountability,” this paper recognizes accountability systems as key to how organizations conceptualize their responsibility to society. The objective is to explore how managers of hybrid organizations conceptualize responsibility and the role of accountability systems in their conceptualization.

Design/methodology/approach

This paper studies hybrid organizations that are for-profit entities with explicitly recognized non-economic imperatives. Semi-structured interviews are conducted with managers of organizations that pursue certification as a B-Corporation, often in conjunction with a legal designation as a benefit corporation.

Findings

Managers of the hybrid organizations evidenced a broader responsibility logic that extends beyond responsibility to shareholders. This pluralistic orientation and broader set of objectives are expressed in a set of certification standards that represent an accountability system that both enables and constrains the way responsibility is understood. The accountability system reflects a “felt” accountability to the “other” manifested, for example, as generational accountability, with the other (re)created relative to the certification standards.

Research limitations/implications

Certifications and standards represent accounting-based accountability systems that produce a type of accountability in which the certification becomes the overall objective nudging out efforts to take accountability-based accounting seriously (Dillard and Vinnari, 2019). At the same time, the hybrids under study, while not perfect exemplars, incline toward an ethic of accountability (Dillard and Brown, 2014) that moves them closer to accountability-based accounting.

Originality/value

The findings reveal perspectives of managers embedded in hybrid organizations, illustrating their experiences of responsibility and accountability systems in practice (Grossiet al., 2019). The insights can be extended to other hybrid contexts where accountability systems may be used to demonstrate multiple performance objectives. We also recognize the irony in the need for an organization to be required to attain a special license to operate in a more responsible manner.
COVID-19 and the neo-liberal paradigm in higher education: changing landscape
Authors: Pan Suyan
Published: October 2020

Purpose

This article aims to provide a timely examination of and reflection on the impact of COVID-19 on the neo-liberal paradigm that has been prevalent in international higher education (HE) for two decades since the late 1990s.

Design/methodology/approach

Methodologically, this paper deploys conceptual mapping as an analytical tool to explore and examine the global news updates that provide timely (i.e. early 2020) record of the fast-moving pandemic.

Findings

It unfolds four pairs of contradictions occurring in the Western universities during the pandemic outbreak, i.e. HE as cross-border services vs border control, the state's shrinking public funding vs universities under financial threat, increased reliance on foreign students' tuition fee vs decreased international enrolment and the user-pays philosophy vs the rising force of user says.

Research limitations/implications

It is argued that the pending crises facing Western universities are not merely financial issues; they reveal the shortcomings that are inherent in business model of HE driven by economic globalisation but triggered by coronavirus pandemic to erupt. The pandemic should be temporary, but its spill-over effects may alter the overarching landscape of the international HE relations, which is part and parcel of the changing geopolitical order featured as de-globalisation.

Practical implications

The paper has practical implications for acting on international HE in the time of coronavirus pandemic. They mainly consider four aspects: (1) travel distance as new determinant of study abroad, (2) the renewed significance of a state's role in policymaking and financial undertaking, (3) shortcomings in market mechanism and (4) East Asia as an emerging regional hub of study abroad.

Social implications

This paper is expected to leverage three lessons learned from the upending situation. First, it is conceptually misleading to define international HE as a form of market-led “transnational service” and cross-border tradeable product undermining a state's control. Second, a state's supervising model needs to be reviewed, to embrace the renewed relationship between a state and universities in the new context of global pandemic. Third, the global landscape of international HE may be altered.

Originality/value

This conceptual paper provides a timely critique of the neo-liberal paradigm in HE and shedding light on the changing global landscape of international HE along with the changing geopolitical relations reshuffled by COVID-19 and its spill-over effects.
Did POM Wonderful leave an aftertaste?
Authors: Johnson Mark Steven
Published: October 2020

Purpose

The purpose of this paper is to determine the impact of the Supreme Court’s ruling that POM Wonderful could sue Coca-Cola, a competitor, for misrepresentation of their products. This decision has the potential to alter the legal environment for soft drink and food processing firms.

Design/methodology/approach

The author conducted an event study of the shareholder value effects of the court decision. The analysis estimates the market responses to the decisions. To control the effects of market-wide fluctuations, the author uses two alternative models of the returns generating process to calculate abnormal returns, the capital asset pricing model (CAPM) and the Fama-French 3-factor models.

Findings

The author hypothesizes that soft drink firms will be negatively impacted by the Supreme Court’s decision, because it may limit their ability to market beverages with a low percentage of expensive juices. Consistent with this argument, the author finds that the stock prices of publicly traded soft drink firms reacted negatively to the announcement of the Supreme Court’s decision. The author also hypothesizes that there may be a spillover effect to food processing firms. These firms may also be at risk to being sued by competitors for exaggerated claims. Contrary to this argument, the author finds no spillover effect to other types of food processing firms. Thus, the decision did leave an aftertaste for the soft drink industry but not the food processing industry.

Originality/value

This study is the first to examine the impact of the right to sue competitors in the food industry for misrepresentation of products.
Examining the mediating role of social interactivity between customer engagement and brand loyalty
Authors: Ting Ding Hooi , Abbasi Amir Zaib , Ahmed Sohel
Published: October 2020

Purpose

This study aims at identifying and examining the mediating role of customer engagement behavior and social interactivity onbrand loyalty.

Design/methodology/approach

A correlational study design was adopted in this study to collect data (online survey) from 400 online participants active on Facebook pages.

Findings

Empirical results reveal that there is a significant and positive impact of social interactivity on consumer engagement behavior and brand loyalty.

Research limitations/implications

The findings would help decision makers to make useful decisions in their everyday work practices, which would ultimately increase the market competition of brands.

Practical implications

Decision makers should focus on the entertainment and interactivity levels in advertisement designs that would allow customers to perceive the novelty of advertising.

Social implications

The results are critical in developing consumers' attitude and perception toward a brand by providing them insights regarding the characteristics of brands.

Originality/value

The participation and social interactivity of consumers on the Facebook page drive consumer engagement behavior and brand loyalty.
Performance improvement of supplier-side e-tender-driven marketing process
Authors: Gupta Piyush , Pranjal Piyush , Bera Sasadhar , Sarkar Soumya , Sachan Amit
Published: October 2020

Purpose

Considerable amount of purchases in business-to-business (B2B) markets make through the tendering process. As technology keeps driving B2B procurement, both the supplier/contractor and buyer firms have settled down in their respective roles in the electronic-tendering environment. Researchers have ignored the supplier-side e-tender-driven marketing process that might lead to substantively successful financial performance. The purpose of this study is to improve the performance of an e-tender-driven marketing process of an original equipment manufacturer (OEM) incorporating the stakeholder's inputs.

Design/methodology/approach

Discrete event simulation modelling (DESM) has been used as a methodology to model, analyse and improve the process with the involvement of stakeholders at every stage of the study. Different scenarios are analysed to identify the near-optimal scenario based on agreed-upon key performance indicators.

Findings

Scenario that incorporated man-power sharing and eliminating avoidable activities gives the near-optimal solution for implementation.

Research limitations/implications

This study highlights that better insights can be gained by adopting the process-oriented view of the marketing–operations interface. Embracing a stakeholder-based consultative approach gives research a more practical outlook and reduces the gap between theory and practice. Suggestions for further research are provided.

Practical implications

B2B organizations, where lines between marketing and operations are blurred, can improve their marketing processes by implementing operations research tools.

Originality/value

This study provides an attempt to improve the performance of a supplier-side e-tender-driven marketing process of an OEM using the DESM methodology incorporating stakeholder's inputs.
On the collective efficacy of social media teams
Authors: Tafesse Wondwesen , Korneliussen Tor
Published: October 2020

Purpose

The purpose of this study is to investigate the contribution of social media teams to firm social media performance. Although social media teams are tasked with planning, executing and optimizing the social media marketing effort of firms, little systematic research has examined their roles. Drawing on social cognitive theory, the present study develops collective social media efficacy as a key mechanism to explain the contribution of social media teams to firm social media performance.

Design/methodology/approach

The study tested a conceptual framework in which social media team members' previous experience, short-term training and online resources use contribute to collective social media efficacy. In turn, collective social media efficacy is hypothesized to enhance firm social media performance. The study employed primary data and PROCESS macro to test its proposed hypotheses.

Findings

The findings revealed that previous social media experience, short-term training and online resources use contributed to firm social media performance by enabling social media teams to build strong collective social media efficacy.

Originality/value

The findings offer novel insights into how firms can optimize their social media marketing effort by systematically managing their social media teams. The findings add to the nascent literature on the organizational influences of social media performance.
Hunters versus hunted: New perspectives on the energetic costs of survival at the top of the food chain
Authors: Williams Terrie M. , Peter‐Heide Jørgensen Mads , Pagano Anthony M. , Bryce Caleb M.
Published: October 2020

Global biotic and abiotic threats, particularly from pervasive human activities, are progressively pushing large, apex carnivorous mammals into the functional role of mesopredator. Hunters are now becoming the hunted. Despite marked impacts on these animals and the ecosystems in which they live, little is known about the physiological repercussions of this role downgrading from ultimate to penultimate predator.

Here we examine how such ecological role reversals alter the physiological processes associated with energy expenditure, and ultimately the cost of survival during peak performance.

Taxonomic group, preferred habitat and domestication affected the capacity of the oxygen pathway to support high levels of aerobic performance by carnivorous mammals. Fear responses associated with anthropogenic threats also impacted aerobic performance.

Allometric trends for three energetic metrics [maximum oxygen consumption, field metabolic rates (FMRs) and the cost per stride or stroke], showed distinct trends in aerobic capacity for different evolutionary lineages of mammalian predators. Cursorial canids that chase down prey demonstrated the highest relative maximum oxygen consumption rates (10–25 times resting levels) and FMRs, while ambush predators (i.e. felids) and diving marine mammals had aerobic capacities that were similar to or lower than sedentary domestic mammals of comparable size.

The maximum energetic cost of performance for apex predators depended on whether the animals were hunters or the hunted. Escape responses were exceptionally costly for marine (narwhal Monodon monoceros) and terrestrial (mountain lion Puma concolor) locomotor specialists, as well as semi‐aquatic (polar bear Ursus maritimus) species; all showed a nearly two‐fold increase in peak energy expenditure when avoiding threats.

As the duration and frequency of threats to wild species continue to grow, cumulative energetic costs are becoming more apparent. In view of this, attention to the energy demands of apex predators will provide vital predictive power to anticipate mismatches between a species' functional design and human‐induced pressures, and allow for the development of conservation strategies based on how species are built to survive.

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