bluuebunny/crossref_metadata_2025 huggingface dataset:
Using the UniFrac metric on Whole Genome Shotgun data
Authors: Wei Wei , Koslicki David
Published: January 2022

The UniFrac metric has proven useful in revealing diversity across metagenomic communities. Due to the phylogeny-based nature of this measurement, UniFrac has historically only been applied to 16S rRNA data. Simultaneously, Whole Genome Shotgun (WGS) metagenomics has been increasingly widely employed and proven to provide more information than 16S data, but a UniFrac-like diversity metric suitable for WGS data has not previously been developed. The main obstacle for UniFrac to be applied directly to WGS data is the absence of phylogenetic distances in the taxonomic relationship derived from WGS data. In this study, we demonstrate a method to overcome this intrinsic difference and compute the UniFrac metric on WGS data by assigning branch lengths to the taxonomic tree obtained from input taxonomic profiles. We conduct a series of experiments to demonstrate that this WGSUniFrac method is comparably robust to traditional 16S UniFrac and is not highly sensitive to branch lengths assignments, be they data-derived or model-prescribed. Code implementing a prototype of WGSUniFrac along with paper reproducible are available at https://github.com/KoslickiLab/WGSUniFrac.
Is mindfulness associated with lower pain reactivity and connectivity of the default mode network? A replication and extension study in healthy and episodic migraine participants
Authors: Hunt Carly , Letzen Janelle E. , Krimmel Samuel R , Burrowes Shana A.B. , Haythornthwaite Jennifer A. , Finan Patrick , Vetter Maria , Seminowicz David A.
Published: January 2022

Formal training in mindfulness-based practices promotes reduced experimental and clinical pain, which may be driven by reduced emotional pain reactivity and undergirded by alterations in the default mode network (DMN), implicated in mind-wandering and self-referential processing. Recent results published in this journal suggest that mindfulness, defined here as the day-to-day tendency to maintain a non-reactive mental state in the absence of training, associates with lower pain reactivity, greater heat-pain thresholds, and resting-state DMN functional connectivity (FC) in healthy adults in a similar manner to trained mindfulness. The extent to which these findings extend to chronic pain samples and replicate in healthy samples is unknown. Using data from healthy adults (n = 36) and episodic migraine patients (n = 98) and replicating previously published methods, we observed no significant association between mindfulness and heat-pain threshold (r = -0.05, p = .80), pain intensity (r = -.02, p = .89) or unpleasantness (r = .02, p = .89), or pain catastrophizing (PC; r = .30, p = .08) in healthy controls, or between mindfulness and headache frequency (r = -.11, p = .26), severity (r = .03, p = .77), impact (r = -.17, p = .10) or PC (r = -0.09, p = .36) in patients. There was no association between DMN connectivity and mindfulness in either sample when probed via seed-based FC analyses. In post-hoc whole brain exploratory analyses, a meta-analytically derived DMN node (i.e., posterior cingulate cortex; PCC) showed connectivity with regions unassociated with pain processing as a function of mindfulness, such that healthy adults higher in mindfulness showed greater PCC-cerebellum FC. Collectively, these findings suggest that the relationship between mindfulness and DMN-FC may be nuanced or lacking in robustness, and cast doubt on mindfulness as a clinically meaningful protective factor in migraine.

Perspective

This study tested relationships between mindfulness and pain, pain reactivity and default mode connectivity in healthy adults and migraine patients. Findings cast doubt on mindfulness as an individual difference marker of the ability to cope with pain in healthy adults, and as a protective factor in episodic migraine.
c-Fos protein shRNA blockade in the central amygdala nucleus interfere with rats emotional reactivity on behavioral and autonomic level
Authors: Robakiewicz Ita
Published: January 2022

This report is focusing on a function of the c-Fos protein in an associative, stress-induced memory. The shRNA vector injections were utilised to functionally silence the central amygdala nucleus in adult Wistar rats. Subsequently the operated animals and their control counterparts were screened in a selection of an emotionally-dependent tests and in a few standard behavioral neuroscience tools. Rats from the c-Fos silencing (ShFos) group expressed contra-depressive-like behaviors in Porsolt Swimming Test, spending more time actively searching for escape way then the rats from the control group. ShFos rats also had engaged in a more rapid activity in the Open Field Test, showing a decline in the neo-phobia. Micturition was decreased in shFos animals, indicating a change in the emotionality on an autonomic level. Presented results are showcasing a multi-directional regulation of the behaviors from the central amygdala nucleus by the c-Fos activity.
Physiological responses of plants to in vivo XRF radiation damage: insights from anatomical, elemental, histochemical, and ultrastructural analyses
Authors: Montanha Gabriel Sgarbiero , Marques João Paulo Rodrigues , Rodrigues Eduardo Santos , Jones Michael W. M. , de Carvalho Hudson Wallace Pereira
Published: January 2022

X-ray fluorescence spectroscopy (XRF) is a powerful technique for the in vivo assessment of plant tissues. However, the potential X-ray exposure damages might affect the structure and elemental composition of living plant tissues leading to artefacts in the recorded data. Herein, we exposed soybean (Glycine max (L.) Merrill) leaves to several X-ray doses through a polychromatic benchtop microprobe X-ray fluorescence spectrometer, modulating the photon flux by adjusting either the beam size, focus, or exposure time. The structure, ultrastructure and physiological responses of the irradiated plant tissues were investigated through light and transmission electron microscopy (TEM). Depending on the dose, the X-ray exposure induced decreased K and X-ray scattering intensities, and increased Ca, P, and Mn signals on soybean leaves. Anatomical analysis indicated necrosis of the epidermal and mesophyll cells on the irradiated spots, where TEM images revealed the collapse of cytoplasm and cell-wall breaking. Furthermore, the histochemical analysis detected the production of reactive oxygen species, as well as inhibition of chlorophyll autofluorescence in these areas. Under certain X-ray exposure conditions, e.g., high photon flux and exposure time, XRF measurements may affect the soybean leaves structures, elemental composition, and cellular ultrastructure, and induce programmed cell death. These results shed light on the characterization of the radiation damage, and thus, help to assess the X-ray radiation limits and strategies for in vivo for XRF analysis.

Highlight

By exposing soybean leaves to several X-ray doses, we show that the characteristic X-ray induced elemental changes stem from plants’ physiological signalling or responses rather than only sample dehydration.
Curcumin and NCLX Inhibitors Share Anti-Tumoral Mechanisms in Microsatellite-Instability-Driven Colorectal Cancer
Authors: Guéguinou Maxime , Ibrahim Sajida , Bourgeais Jérôme , Robert Alison , Pathak Trayambak , Zhang Xuexin , Crottès David , Dupuy Jacques , Ternant David , Monbet Valérie , Guibon Roseline , Flores-Romero Hector , Lefèvre Antoine , Lerondel Stéphanie , Le Pape Alain , Dumas Jean-François , Frank Philippe G. , Girault Alban , Chautard Romain , Guéraud Françoise , García-Sáez Ana J. , Ouaissi Mehdi , Emond Patrick , Sire Olivier , Hérault Olivier , Fromont-Hankard Gaëlle , Vandier Christophe , Tougeron David , Trebak Mohamed , Raoul William , Lecomte Thierry
Published: January 2022

Colorectal cancer (CRC) is associated with high mortality worldwide and new targets are needed to overcome treatment resistance. Recent evidences highlight a role of the mitochondria calcium homeostasis in the development of CRC. In this context, we aimed to evaluate the role of the mitochondrial sodium-calcium-lithium exchanger (NCLX) and its targeting in CRC. We also identified curcumin as a new potential inhibitor of NCLX.

In vitro, curcumin exerted strong anti-tumoral activity through its action on NCLX with mtCa2+ and reactive oxygen species overload associated with a mitochondrial membrane depolarization, leading to reduced ATP production and apoptosis through mitochondrial permeability transition pore opening concomitant with G2/M cell cycle arrest. NCLX inhibition with either CGP37157 (a benzodiazepine derivative), small interfering RNA-mediated knock-down or knockout approaches reproduced the effects of curcumin. Altered mitochondrial respiration, cellular aerobic glycolysis and endoplasmic reticulum–mitochondria membrane perturbations participated in these mechanisms. In a xenograft mouse model, NCLX inhibitors decreased CRC tumor growth. Both transcriptomic analysis of The Cancer Genome Atlas dataset and immunohistochemical analysis of tissue microarrays from 381 patients with microsatellite instability (MSI)-driven CRC demonstrated that higher NCLX expression was associated with MSI status and for the first time NCLX expression was significantly associated with recurrence-free survival in MSI CRC patients.

Our findings provide strong evidence that blocking NCLX inhibits CRC in vitro and in vivo. We highlight a novel anti-tumoral mechanism of curcumin through its action on NCLX and mitochondria calcium overload that could benefit for therapeutic treatment of patients with MSI CRC.
Septins Provide Microenvironment Sensing and Cortical Actomyosin Partitioning in Motile Amoeboid T Lymphocytes
Authors: Zhovmer Alexander S. , Manning Alexis , Smith Chynna , Sáez Pablo J. , Ma Xuefei , Tsygankov Denis , Cartagena-Rivera Alexander X. , Singh Rakesh K. , Tabdanov Erdem D.
Published: January 2022

The all-terrain motility of lymphocytes in tissues and tissue-like gels is best described as amoeboid motility. For amoeboid motility, lymphocytes do not require specific biochemical or structural modifications to the surrounding extracellular matrix. Instead, they rely on changing shape and steric interactions with the microenvironment. However, the exact mechanism of amoeboid motility remains elusive. Here we report that septins shape T cells for amoeboid motility. Specifically, septins form F-actin and alpha-actinin-rich cortical rings at the sites of cortex-indenting collisions of T cells with the extracellular matrix. Cortical rings compartmentalize cells into chains of spherical segments that are spatially conformed to the available lumens, forming transient ‘hourglass’-shaped steric locks onto the surrounding collagen fibers. The steric lock facilitates pressure-driven peristaltic propulsion of cytosolic content by individually contracting cell segments. Our results demonstrate that septins provide microenvironment-guided partitioning of actomyosin contractility and steric pivots for amoeboid motility of T cells in tissue-like microenvironments.

GLOSSARY

Steric interactions - interactions by the means of their spatial collision dependent on objects’ shapes.

Steric guidance - cell navigation within crowded 3D environments, determined by the available passages around and between steric hindrances.

Peristaltic treadmilling - locomotion mode by the means of a repeated sequence of polarized cell cortex extension, stabilization, and retraction, accompanied by translocation of nucleus and cytoplasmviacircumferential cortex contractility.

Significance Statement

T cells can be highly motile, searching for cognate antigens or better yet targets in chimeric antigen receptor therapy settings. However, mechanisms of motility remain elusive for T cells migrating in structurally and biochemically diverse tissues. Here we address one pivotal question of basic and clinical immunology - How T cells achieve the ‘all-terrain’ motility? Here we decipher and report septin-based T cell motility in a 3D tissue-like environment. Specifically, we show that septins facilitate cell morphological responsiveness to the steric obstacles,i.e., collagen fiber-wise partitioning of actomyosin cortex contractility and cell-obstacle steric interactions. These responses coordinate peristaltic propulsion of the lymphocyte’s cytosolic content along its individually contracting cell segments, forming the obstacle-avoiding motility,i.e.,circumnavigation, shared across various tested lymphocytes.
Profiling of the human intestinal microbiome and bile acids under physiologic conditions using an ingestible sampling device
Authors: Shalon Dari , Culver Rebecca Neal , Grembi Jessica A. , Folz Jacob , Treit Peter , Dethlefsen Les , Meng Xiandong , Yaffe Eitan , Spencer Sean , Shi Handuo , Aranda-Díaz Andrés , Patterson Andrew D. , Triadafilopoulos George , Holmes Susan P. , Mann Matthias , Fiehn Oliver , Relman David A. , Huang Kerwyn Casey
Published: January 2022

The spatiotemporal structure of the human microbiome and metabolome reflects and determines regional intestinal physiology and may have implications for disease. Yet, we know little about the distribution of microbes and their products in the gut because of reliance on stool samples and limited access only to some regions of the gut using endoscopy in fasting or sedated individuals. To address these deficiencies, we developed and evaluated a safe, ingestible device that collects samples from multiple regions of the human intestinal tract during normal digestion. The collection of 240 intestinal samples from 15 healthy individuals using the device revealed significant differences between microbes and metabolites present in the intestines versus stool. Certain microbial taxa were differentially enriched, and bile acid profiles varied along the intestines and were highly distinct from those of stool. Correlations between gradients in bile acid concentrations and microbial abundance predicted species that altered the bile acid pool through deconjugation. Overall, we identified heterogeneous intestinal profiles of bacterial taxa and metabolites indicating that non-invasive multi-regional sampling of the intestinal tract under physiological conditions can help elucidate the roles of the gut microbiome and metabolome in human physiology and disease.
Membrane-mediated interactions between hinge-like particles
Authors: Li Bing , Abel Steven M.
Published: January 2022

Adsorption of nanoparticles on a membrane can give rise to interactions between particles, mediated by membrane deformations, that play an important role in self-assembly and membrane remodeling. Previous theoretical and experimental research has focused on nanoparticles with fixed shapes, such as spherical, rod-like, and curved nanoparticles. Recently, hinge-like DNA origami nanostructures have been designed with tunable mechanical properties. Inspired by this, we investigate the equilibrium properties of hinge-like particles adsorbed on an elastic membrane using Monte Carlo and umbrella sampling simulations. The configurations of an isolated particle are influenced by competition between bending energies of the membrane and the particle, which can be controlled by changing adsorption strength and hinge stiffness. When two adsorbed particles interact, they effectively repel one another when the strength of adhesion to the membrane is weak. However, a strong adhesive interaction induces an effective attraction between the particles, which drives their aggregation. The configurations of the aggregate can be tuned by adjusting the hinge stiffness: Tip-to-tip aggregation occurs for flexible hinges, whereas tip-to-middle aggregation also occurs for stiffer hinges. Our results highlight the potential for using the mechanical features of deformable nanoparticles to influence their self-assembly when the particles and membrane mutually influence one another.
FoodMicrobionet v4: a large, integrated, open and transparent database for food bacterial communities
Authors: Parente Eugenio , Zotta Teresa , Ricciardi Annamaria
Published: January 2022

With the availability of high-throughput sequencing techniques our knowledge of the structure and dynamics of food microbial communities has made a quantum leap. However, this knowledge is dispersed in a large number of papers and hard data are only partly available through powerful on-line databases and tools such as QIITA, MGnify and the Integrated Microbial Next Generation Sequencing platform, whose annotation is not optimized for foods.

Here, we present the 4th iteration of FoodMicrobionet, a database of the composition of bacterial microbial communities of foods and food environments. With 180 studies and 10,151 samples belonging to 8 major food groups FoodMicrobionet 4.1.2 is arguably the largest and best annotated database on food bacterial communities. This version includes 1,684 environmental samples and 8,467 food samples, belonging to 16 L1 categories and 196 L6 categories of the EFSA FoodEx2 classification and is approximately 4 times larger than previous version (3.1, https://doi.org/10.1016/j.ijfoodmicro.2019.108249).

Using data in FoodMicrobionet we confirm that taxonomic assignment at the genus level can be performed confidently for the majority of amplicon sequence variants using the most commonly used 16S RNA gene target regions (V1-V3, V3-V4, V4), with best results with higher quality sequences and longer fragment lengths, but that care should be exercised in confirming the assignment at species level.

Both FoodMicrobionet and related data and software conform to FAIR (findable, accessible, interoperable, reusable/reproducible) criteria for scientific data and software and are freely available on public repositories (GitHub, Mendeley data).

Even if FoodMicrobionet does not have the sophistication of QIITA, IMNGS and MGnify, we feel that this iteration, due to its size and diversity, provides a valuable asset for both the scientific community and industrial and regulatory stakeholders.
High abundance of transcription regulators compacts the nucleoid in Escherichia coli
Authors: Yilmaz Cihan , Schnetz Karin
Published: January 2022

In enteric bacteria organization of the circular chromosomal DNA into a highly dynamic and toroidal shaped nucleoid involves various factors such as DNA supercoiling, nucleoid-associated proteins (NAPs), the structural maintenance of chromatin (SMC) complex, and macro-domain organizing proteins. Here we show that ectopic expression of transcription regulators at high levels leads to nucleoid compaction. This serendipitous result was obtained by fluorescence microscopy upon ectopic expression of the transcription regulator and phosphodiesterase PdeL of Escherichia coli of a strain expressing the mCherry-tagged HU-α subunit (HupA) for nucleoid staining. Nucleoid compaction by PdeL depends on DNA-binding, but not on its enzymatic phosphodiesterase activity. Nucleoid compaction was also observed upon high-level ectopic expression of the transcription regulators LacI, RutR, RcsB, LeuO and Cra, which range from single target gene regulators to global regulators. In case of LacI its high-level expression in presence of the gratuitous inducer IPTG also led to nucleoid compaction indicating that compaction is caused by unspecific DNA-binding. In all cases nucleoid compaction correlated with misplacement of the FtsZ ring and loss of MukB foci, a subunit of the SMC complex. Thus, high levels of several transcription regulators cause nucleoid compaction with consequences on transcription, replication, and cell division.

Importance

The bacterial nucleoid is a highly organized and dynamic structure for simultaneous, transcription, replication and segregation of the bacterial genome. Compaction of the nucleoid and disturbance of DNA segregation and cell division by artificially high levels of transcription regulators, as described here, reveals that an excess of DNA-binding protein disturbs nucleoid structuring. The results suggest that ectopic expression levels of DNA-binding proteins for genetic studies of their function but also for their purification should be carefully controlled and adjusted.
Hurricane Harvey Impacts on Water Quality and Microbial Communities in Houston, TX Waterbodies
Authors: LaMontagne Michael G. , Zhang Yan , Guillen George J. , Gentry Terry J. , Allen Michael S.
Published: January 2022

Hurricanes, and other extreme weather events, can temporarily alter the structure of coastal systems and generate floodwaters that are contaminated with fecal-associated microbes; however, every coastal system and extreme weather event is unique, so identification of trends and commonalities in these episodic events is challenging. To improve our understanding of the resilience of coastal systems to the disturbance of extreme weather events and the risk exposure to floodwaters poses to the public, we monitored water quality, fecal indicator bacteria (FIB) at three stations within Clear Lake, an estuary between Houston and Galveston, and three stations in bayous that feed into the estuary. Water samples were collected immediately before Hurricane Harvey (pre-HH, August 25th, 2017), immediately after (HH, August 30th) and then throughout the fall of 2017 (post-HH). FIB levels were monitored by culturing E. coli and Enterococci. Microbial community structure was profiled by high throughput sequencing of PCR-amplified 16S rRNA gene fragments. Water quality and FIB data was also compared to historical data for these water body segments. Before Harvey, salinity within Clear Lake ranged from 9 to 11 practical salinity units (PSU). Immediately after the storm, salinity dropped to < 1 PSU and then gradually increased to pre-storm and historical levels over two months. Dissolved inorganic nutrient levels were also relatively low immediately after Harvey and returned, within a couple of months, to pre-HH and historical levels. FIB levels were elevated immediately after the storm; however, after one week, E. coli levels had decreased to acceptable levels for freshwater. Enterococci levels collected several weeks after the storm were within the range of historical levels for these water bodies. Microbial community structure shifted from a system dominated by Cyanobacteria sp. before HH to a system dominated by Proteobacteria and Bacteroidetes immediately after. Further, several sequences observed only in floodwater showed similarity to sequences previously reported for samples collected following Hurricane Irene. These changes in beta diversity corresponded to salinity and nitrate/nitrite concentrations. Differential abundance analysis of metabolic pathways, predicted from 16S sequences, suggested that pathways associated with virulence and antibiotic resistance were elevated in floodwater. Overall, these results suggest that recovery of the Clear Lake system following Hurricane Harvey took at least a month and floodwater generated from these extreme events may have high levels of fecal contamination, antibiotic resistant bacteria and bacteria rarely observed in other systems.
m6A reader Pho92 is recruited co-transcriptionally and couples translation efficacy to mRNA decay to promote meiotic fitness in yeast
Authors: Varier Radhika A. , Sideri Theodora , Capitanchik Charlotte , Manova Zornitsa , Calvani Enrica , Rossi Alice , Edupuganti Raghu R. , Ensinck Imke , Chan Vincent W.C. , Patel Harshil , Kirkpatrick Joanna , Faull Peter , Snijders Ambrosius P. , Vermeulen Michiel , Ralser Markus , Ule Jernej , Luscombe Nicholas M. , van Werven Folkert J.
Published: January 2022

N6-methyladenosine (m6A) RNA modification impacts mRNA fate primarily via reader proteins, which dictate processes in development, stress, and disease. Yet little is known about m6A function in Saccharomyces cerevisiae, which occurs solely during early meiosis. Here we perform a multifaceted analysis of the m6A reader protein Pho92/Mrb1. Cross-linking immunoprecipitation analysis reveals that Pho92 associates with the 3’end of meiotic mRNAs in both an m6A-dependent and independent manner. Within cells, Pho92 transitions from the nucleus to the cytoplasm, and associates with translating ribosomes. In the nucleus Pho92 associates with target loci through its interaction with transcriptional elongator Paf1C. Functionally, we show that Pho92 promotes and links protein synthesis to mRNA decay. As such, the Pho92-mediated m6A-mRNA decay is contingent on active translation and the CCR4-NOT complex. We propose that the m6A reader Pho92 is loaded co-transcriptionally to facilitate protein synthesis and subsequent decay of m6A modified transcripts, and thereby promotes meiosis.
The CRISPR-Cas System differentially regulates surface-attached and pellicle-biofilm in Salmonella enterica serovar Typhimurium
Authors: Sharma Nandita , Das Ankita , Raja Pujitha , Marathe Sandhya Amol
Published: January 2022

CRISPR-Cas (Clustered Regularly Interspaced Short Palindromic Repeats-CRISPR associated) system has been studied for its role in biofilm regulation and expression of outer membrane proteins in Salmonella. We investigated the CRISPR-Cas mediated biofilm regulation in Salmonella enterica serovar Typhimurium by deleting CRISPR-Cas components, ΔcrisprI, ΔcrisprII, ΔΔcrisprI crisprII, and Δcas op. We determined that the system positively regulates surface-biofilm while inhibiting pellicle-biofilm. In knockout strains, flagellar (fliC, flgK) and curli (csgA) genes were repressed, causing reduced surface-biofilm. Conversely, they displayed altered pellicle-biofilm architecture possessing bacterial multilayers and a denser ECM with enhanced cellulose and lesser Curli, ergo weaker pellicle. The intracellular cellulose concentration was less in the knockout strains due to upregulation of bcsC, necessary for cellulose export. We hypothesized that exported cellulose integrates into the pellicle. We determined that crp is upregulated in the knockout strains, thereby inhibiting the expression of csgD, hence csgA and bcsA. The conflicting upregulation of bcsC, the last gene of bcsABZC operon, could be independently regulated by the CRISPR-Cas system owing to a partial match between the CRISPR-spacers and bcsC gene. The CRP-mediated regulation of the flagellar genes in the knockout strains was probably circumvented through the regulation of Yddx governing the availability of σ28 factor that further regulates class3 flagellar genes (fliC, flgK). Additionally, the variations in the LPS profile and expression of LPS-related genes (rfaC, rfbG, rfbI) in the knockout strains could also contribute to the altered pellicle architecture. Collectively, we establish that the CRISPR-Cas system differentially regulates the formation of surface-attached and pellicle-biofilm.
Identification and characterization of a dlx2b cis-regulatory element both sufficient and necessary for correct transcription during zebrafish tooth development
Authors: Jackman William R. , Moon Yujin , Anderson Drew R. , DeFusco Audrey A. , Nguyen Vy M. , Liu Sarah Y. , Carter Elisabeth H. , Littleford Hana E. , Richards Elizabeth K. , Jowdry Andrea L.
Published: January 2022

Much remains to be learned about how cis-regulatory elements such as enhancers function, especially during vertebrate organ development. To increase knowledge in this area, we have examined the cis-regulation of the transcription factor dlx2b during zebrafish larval tooth formation. We have created a GFP knock-in line that replicates dlx2b expression during tooth development and have also isolated a minimal enhancer of dlx2b (MTE1) sufficient for activating most of the tooth germ expression pattern. We have found that four evolutionarily conserved predicted transcription factor binding sites are required for the function of this minimal enhancer in both contexts. When the conserved sequences are mutated in a transgene it eliminates the activity of the enhancer and when they are deleted at the dlx2b locus it causes a dramatic alteration in the expression pattern. We hypothesize that disabling this enhancer at the dlx2b locus may be enabling other nearby cis-regulatory elements to take control of the promoter. These experiments reveal details of how cis-regulatory elements are working to control gene expression during organogenesis and highlight how much remains to be learned by empirical studies of gene regulation.

Graphical Abstract
Scleraxis-lineage cells are required for tendon homeostasis and their depletion induces an accelerated extracellular matrix aging phenotype
Authors: Korcari Antonion , Nichols Anne EC. , Buckley Mark R. , Loiselle Alayna E.
Published: January 2022

Aged tendons have disrupted homeostasis, increased injury risk, and impaired healing capacity. Understanding mechanisms of homeostatic disruption is crucial for developing therapeutics to retain tendon health through the lifespan. Here, we developed a novel model of accelerated tendon extracellular matrix (ECM) aging via depletion of Scleraxis-lineage (ScxLin) cells in young mice (DTR). DTR recapitulates many aspects of tendon aging including comparable declines in cellularity, alterations in ECM structure, organization, and composition. Single cell RNA-sequencing demonstrated a conserved decline in tenocytes associated with ECM biosynthesis in aged and DTR tendons, identifying the requirement for ScxLin cells during homeostasis. However, the remaining cells in aged and DTR tendons demonstrate functional divergence. Aged tenocytes become pro-inflammatory and lose proteostasis. In contrast, DTR tenocytes demonstrate enhanced remodeling capacity. Collectively, this study defines DTR a novel model of accelerated tendon ECM aging and identifies novel biological intervention points to maintain tendon function through the lifespan.
The kinase inhibitor Palbociclib is a potent and specific RNA-binding molecule
Authors: Shortridge Matthew D. , Vidalala Venkata , Varani Gabriele
Published: January 2022

The growing awareness of the role of RNA in human disease has motivated significant efforts to discover drug-like small molecules that target RNA. However, high throughput screening campaigns report very low hit rates and generally identify compounds with weak affinity, while most structures reported in Academic studies also lack the pharmacological properties of successful drugs. Even FDA-approved RNA-targeting drugs have only weak (10 μM) binding activity. Thus, it is often stated that only complex RNA structures, such as the ribosome or riboswitches, are amenable to small molecule chemistry. We report that the kinase inhibitor Palbociclib/Ibrance is a nM ligand for the HIV-1 TAR. It inhibits recruitment of the positive transcription elongation factor complex at nM concentrations and discriminates >20 fold. We further show that RNA binding can be fully decoupled from kinase inhibition, yielding a new molecule with even higher affinity for RNA. We thus demonstrate that nM affinity, specificity, and potent biochemical activity against ‘undruggable’ RNAs can be found in the chemical space of blockbuster drugs.
Enhanced beamforming techniques for cylindrical-substrate microstrip array antennas
Authors: Exadaktylos Christos P. , Karatzidis Dimitrios I. , Zygiridis Theodoros T. , Kantartzis Nikolaos V.
Published: January 2022

Purpose

A class of robust and efficient beamforming methods is developed in this paper for the optimised design of realistic microstrip antennas on arbitrarily curved substrates. More specifically, this paper aims to focus on the formulation of an effective and computationally light beamforming algorithm and its implementation on a novel realistic cylindrical-substrate microstrip array antenna with significantly decreased size, wideband operation and enhanced radiation characteristics.

Design/methodology/approach

The proposed multi-parametric schemes introduce an efficient null-steering concept, which drastically annihilates the undesired beamformer waveform artefacts, while retaining the real output signal undistorted. In particular, the key objective is the accurate calculation of the appropriate complex feeding weights, required to set nulls along the propagation directions of the unwanted signals and a maximum towards the propagation direction of the desired incoming signal. The featured technique, combined with a modified finite element method, is applied to the design of a new family of cylindrical-substrate microstrip array antennas.

Findings

Numerical results, mainly concerning customisable three-dimensional radiation patterns and attributes, certify the merits of the algorithm and its limited system demands. The introduced beamforming algorithms are applied to a variety of different inputs (desired radiation patterns), which indicate that the designed cylindrical-substrate antenna overwhelms existing designs in terms of computational cost for the beamforming algorithm, while retaining acceptable values for radiation characteristics, such as gain, directivity and side-lobe suppression. In this manner, the effectiveness of the prior methodology and the benefits of this newly shaped array antenna are comprehensively revealed and substantiated.

Originality/value

Rigorous beamforming techniques in conjunction with a class of contemporary array antennas are developed for potential use in high-end communication systems, such as 5G configurations. The proposed cylindrical-shaped structures are systematically designed, with an emphasis on space efficiency and wideband radiation effectiveness to offer fully adjustable setups. To this aim, the cylindrical-substrate microstrip antenna, because of its inherent azimuthal symmetry and confined overall dimensions, provides reliable operation and promising performance.
Response to COVID-19: disruption-oriented, flexible networks, risk and resilience
Authors: Wooderson Cheyne M.
Published: January 2022

Purpose

This study assesses disruption risk management and resilience capabilities from the perspective of top-level operations and supply chain managers when faced with COVID-19 disruptions.

Design/methodology/approach

The study involves qualitative research via a triple-phase, interview-based method, following an interpretivist philosophy embodying an empathetic, subjective view to interpret the perspective of top-level managers. The data has been coded and analysed thematically.

Findings

Based on the ability to adapt to changing and uncertain environments using quick decision-making, technology and access to resources, the findings show a level of resilience adequate to withstand risk disruptions. The data do not expose differences between disruption management and traditional risk management but do display potential for businesses to adopt a disruption-oriented supply network that is flexible.

Research limitations/implications

Currently, there are little data concerning COVID-19 disruption risk, and the propagation of these impacts throughout the supply chain. This study is limited to the perspective of top, senior-level managers in supply chain and operations.

Practical implications

The research signifies that by adopting a disruption-oriented, flexible network, business may have the means to overcome and surpass impacts from disruption risks. The study offers knowledge on supply chain resilience and flexibility in times of crisis. Managers and practitioners might adopt the evidence to support in developing strategies towards building resilient supply chains.

Originality/value

The findings and conclusions of this paper are the product of the authors’ own work, and the research has been supported appropriately through academic contributions in the study area. All sources have been acknowledged.
Artificial intelligence and information management in the energy transition of India: lessons from the global IT heart
Authors: Chawla Yash , Shimpo Fumio , Sokołowski Maciej M.
Published: January 2022

Purpose

India is a fast-growing economy, that has a majority share in the global information technology industry (IT). Rapid urbanisation and modernisation in India have strained its energy sector, which is being reformed to cope. Despite being the global IT heart and having above average research output in the field of artificial intelligence (AI), India has not yet managed to leverage its benefits to the full. This study aims to address the role of AI and information management (IM) in India’s energy transition to highlight the challenges and barriers to its development and use in the energy sector.

Design/methodology/approach

The study, through analysis of proposed strategies, current policies, available literature and reports, discusses the role of AI and IM in the energy transition in India, highlighting the current situation and challenges.

Findings

The results show dispersed research and development incentives for IT in the Indian energy sector; however, the needed holistic top-down approach is lacking, calling for due attention in this matter. Adaptive and swift actions from policymakers towards AI and IM are warranted in India.

Practical implications

The ongoing transition of the Indian energy sector with the integration of smart technologies would result in increased access to big data. Extracting the maximum benefits from this would require a comprehensive AI and IM policy.

Social implications

The revolution in AI and robotics must be carried out in line with sustainable development goals, to support climate action and to consider privacy issues – both areas in India must be strengthened.

Originality/value

The paper offers an original discussion on certain applicable solutions regarding the energy transition of AI coming from the Global South; they are based on lessons learned from the Indian case studies presented in this study.
Intrinsic interference suppressed FBMC QAM for MU-MIMO systems in computing and communications
Authors: Y.K. Shobha , H.G. Rangaraju
Published: January 2022

Purpose

In order to optimize BER and to substantiate performance measures, initially, the filter bank multicarrier (FBMC) quadrature amplitude modulation (QAM) performance metrics are evaluated with the cyclic prefix-orthogonal frequency division multiplexing (CP-OFDM) system. The efficiency of CP-OFDM, as well as FBMC/QAM that is transmitting over specific fading channels, is evaluated in terms of quality trade-off metrics over bit error rate (BER) as well as modulation order. When compared with the traditional FBMC systems, the proposed FBMC QAM system shows better performance. The performance metrics of FBMC/QAM with the inclusion of multiuser multiple-input-multiple-output (MUMIMO) is validated with worst case channel environment. The performance penalty gap that exists in CP- OFDM is compared with improved FBMC QAM in terms of both BER and OOB radiation measures. The BER trade off comparison between ML and MMSE optimally determine the prominent signal detection model for high performance FBMC QAM system.

Design/methodology/approach

The main objective of this research work is to provide perceptions about performance, co-channel interference avoidance as well as about the techniques that are used for minimizing the complexity of the system that is related to FBMC QAM structure for reducing intrinsic interference with higher spectral features as well as maximal likelihood (ML) detector systems.

Findings

This research work also looks at the efficiency of multiuser multiple-input-multiple-output (MU-MIMO) FBMC/QAM over nonlinear channels. Furthermore, when compared with OFDM, it also significantly reduces the penalty gap efficiency, thereby enabling the accessibility of the proposed FBMC QAM system from BER as well as implementation point of view. Finally, the signal detection is facilitated by the sub-detector and is achieved on the downlink side by making use of threshold-driven statistical measures that accurately minimize the complexity trade-off measures of the ML detector over modulation order. The computation of the proposed FBMC method’s BER performance measures was carried out through MATLAB simulation environments, as well as efficiency of the suggested work was demonstrated through detailed analyses.

Originality/value

This research work intend to combine the efficient MU-MIMO based transmission scheme with optimal FBMC/QAM for improved QoS over highly nonlinear channels which includes both delay spread and Doppler effects. And optimal signal detection model is facilitated at the downlink side by making use of threshold-driven statistical measures that accurately minimize the complexity trade-off measures of the ML detector over modulation order. The computation of the proposed FBMC method’s BER performance measures was carried out through MATLAB simulation environments, as well as efficiency of the suggested work was demonstrated through detailed analyses.
Personalized content recommendation in online health communities
Authors: Yang Hangzhou , Gao Huiying
Published: January 2022

Purpose

Recommending suitable content for users of online health communities (OHCs) is critical for overcoming information overload problem and facilitate medical decision making, but remains not fully investigated. This study aims to provide a content recommendation approach to automatically match valuable health-related information for OHC members.

Design/methodology/approach

A framework of health-related content recommendation was proposed by leveraging rich social information in online communities. The authors constructed user influence relationship (UIR) utilizing users' interaction records, user profiles and user-generated content. The initial user rating matrix and the user post matching matrix were then created by analyzing text content of posts. Finally, the user rating matrix and the recommended content were generated for community members. Datasets were collected from an OHC to evaluate the effectiveness of the proposed approach.

Findings

The experimental results revealed that the proposed method statistically outperformed baseline models in content recommendation for users of OHCs.

Research limitations/implications

The incorporation of social information can significantly enhance the performance of content recommendation in OHCs. The user post matching degree based on text analysis can improve the effectiveness of recommendation.

Practical implications

This study potentially contributes to the social support exchange and medical decision making of community members and the sustainable prosperity of OHCs.

Originality/value

This study proposes a novel social content recommendation method for online health consumers based on UIRs by leveraging social information in OHCs. The results indicate the significance of social information in content recommendation of healthcare social media.
Supply chain relational capital for sustainability through governance: the moderating effect of network complexity
Authors: Chowdhury Md Maruf Hossan , Chowdhury Mesbahuddin , Khan Eijaz Ahmed , Sajib Shahriar
Published: January 2022

Purpose

This study aims to investigate the conditional direct and indirect effects of supply chain relational capital (RC) on supply chain sustainability via sustainability governance.

Design/methodology/approach

In line with the study’s aims, a quantitative survey-based approach was adopted. This study uses a random sample of 272 manufacturing firms from the apparel industry in Bangladesh. This study assesses the measurement model using partial least square-based structural equation modelling and test the proposed hypotheses using the Hayes PROCESS.

Findings

The results reveal that the indirect effect of supply chain RC on supply chain sustainability via sustainability governance is significant. While at low levels of network complexity (NC), the conditional indirect effect of supply chain RC on supply chain sustainability via sustainability governance is significant, this study finds that such indirect effects are insignificant at high levels of NC. This study further shows that NC positively moderates the relationship between supply chain RC and supply chain sustainability.

Originality/value

While previous studies have demonstrated the role of RC in adopting sustainability practice, this study explores this link further by investigating the conditional direct and indirect effects of supply chain relational capital on supply chain sustainability via sustainability governance.
Ecological inference using data from accelerometers needs careful protocols
Authors: Garde Baptiste , Wilson Rory P. , Fell Adam , Cole Nik , Tatayah Vikash , Holton Mark D. , Rose Kayleigh A. R. , Metcalfe Richard S. , Robotka Hermina , Wikelski Martin , Tremblay Fred , Whelan Shannon , Elliott Kyle H. , Shepard Emily L. C.
Published: January 2022

Accelerometers in animal‐attached tags are powerful tools in behavioural ecology, they can be used to determine behaviour and provide proxies for movement‐based energy expenditure. Researchers are collecting and archiving data across systems, seasons and device types. However, using data repositories to draw ecological inference requires a good understanding of the error introduced according to sensor type and position on the study animal and protocols for error assessment and minimisation.

Using laboratory trials, we examine the absolute accuracy of tri‐axial accelerometers and determine how inaccuracies impact measurements of dynamic body acceleration (DBA), a proxy for energy expenditure, in human participants. We then examine how tag type and placement affect the acceleration signal in birds, using pigeons Columba livia flying in a wind tunnel, with tags mounted simultaneously in two positions, and back‐ and tail‐mounted tags deployed on wild kittiwakes Rissa tridactyla. Finally, we present a case study where two generations of tag were deployed using different attachment procedures on red‐tailed tropicbirds Phaethon rubricauda foraging in different seasons.

Bench tests showed that individual acceleration axes required a two‐level correction to eliminate measurement error. This resulted in DBA differences of up to 5% between calibrated and uncalibrated tags for humans walking at a range of speeds. Device position was associated with greater variation in DBA, with upper and lower back‐mounted tags varying by 9% in pigeons, and tail‐ and back‐mounted tags varying by 13% in kittiwakes. The tropicbird study highlighted the difficulties of attributing changes in signal amplitude to a single factor when confounding influences tend to covary, as DBA varied by 25% between seasons.

Accelerometer accuracy, tag placement and attachment critically affect the signal amplitude and thereby the ability of the system to detect biologically meaningful phenomena. We propose a simple method to calibrate accelerometers that can be executed under field conditions. This should be used prior to deployments and archived with resulting data. We also suggest a way that researchers can assess accuracy in previously collected data, and caution that variable tag placement and attachment can increase sensor noise and even generate trends that have no biological meaning.
World Health Organization global air quality guideline recommendations: Executive summary
Authors: Goshua Anna , Akdis Cezmi A. , Nadeau Kari C.
Published: January 2022

Air pollution is a leading cause of death globally and has resulted in the loss of millions of healthy years of life. Moreover, the health burden has fallen disproportionately upon people in many low‐ and middle‐income countries, where air quality continues to deteriorate. To assist authorities and civil society in improving air quality, World Health Organization has published the first global update to its 2005 air quality guidelines based on a significantly improved body of evidence. To facilitate the implementation of the World Health Organization Global Air Quality Guideline recommendations, this article summarizes the purpose and rationale of the quantitative air quality guidelines and interim target levels for six key pollutants: particulate matter 2.5, particulate matter 10, sulfur dioxide, nitrogen dioxide, ozone, and carbon monoxide. In addition, good practice statements are established for the management of pollutants of concern that lack sufficient evidence to substantiate numerical targets.