bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

AbstractN6-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

AbstractCRISPR-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

AbstractMuch 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

AbstractAged 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

AbstractThe 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

PurposeIndia 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/approachThe 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.FindingsThe 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 implicationsThe 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 implicationsThe 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/valueThe 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

PurposeRecommending 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/approachA 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.FindingsThe experimental results revealed that the proposed method statistically outperformed baseline models in content recommendation for users of OHCs.Research limitations/implicationsThe 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 implicationsThis study potentially contributes to the social support exchange and medical decision making of community members and the sustainable prosperity of OHCs.Originality/valueThis 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

PurposeThis 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/approachIn 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.FindingsThe 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/valueWhile 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

Abstract

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.