bluuebunny/crossref_metadata_2025 huggingface dataset:
Effect of Increasing Glucose Concentration on Estimation of Electrolytes by ion selective electrode
Authors: Khidir Omalkhair A. , Osman Mohammed Elsheikh
Published: November 2020

Background

The measurement of serum electrolytes like sodium (Na+), potassium (K+) is routinely performed in clinical biochemistry laboratories using ion-selective electrodes (ISE).

Aim

To minimize error and test the effect of increasing glucose concentration on estimation of sodium and potassium.

Materials and Methods

Randomly selected sera samples submitted for routine biochemical estimations were pooled for the study. A stock solution of glucose with concentration of 20 g/ dL was prepared by dissolving anhydrous glucose in normal saline (0.9 % NaCl). Next the pooled sera was divided into several aliquots with 1.0 ml sera each and increasing amounts of the stock solution were added to the different aliquots so as to generate glucose concentrations ranging from around 100 mg/dL to about 3000 mg/dL.

Results

the glucose concentration of different serum aliquots obtained on cobas c311(roche system) were found to rang from 110 to 2577 mg/dl. The mean of sodium by direct ion selective 142±0.52 mmol/l, values showed in significant difference (p=0.320).The mean of sodium by indirect ion selective 143 ± 0.72 mmol/l, values showed significant difference (p< 0.05). And the mean of potassium by direct ion selective 3.54 ±0.29 mmol/l, values showed significant difference (p< 0.05).

The mean of potassium by indirect ion selective 3.53±0.26 mmol/l, values showed significant difference (p< 0.05).

Conclusions

Increasing blood gluose interferance in electrlytes mainly potasssium by both direct and indirect ion selective electrode, whenincreasing glucose potassium decreae significantly No different significant between direct and indirect ion selective electrods in potassium when used cobas c311 and easy lyte.Significant interferance in sodium by indirect ion selective electrodewhile no significant interferance in sodium direct ion selective electrode.Glucose concentration interfer the electrolyte specially potassium in concentration more than 1700 mg/dl by direct and indirect methods.
Sodium Pyruvate Ameliorates Influenza A Virus InfectionIn Vivo
Authors: Reel Jessica M. , Lupfer Christopher R.
Published: November 2020

Influenza A virus (IAV) causes seasonal epidemics annually and pandemics every few decades. Most antiviral treatments used for IAV are only effective if administered during the first 48 hours of infection and antiviral resistance is possible. Therapies that can be initiated later during IAV infection and that are less likely to elicit resistance will significantly improve treatment options. Pyruvate, a key metabolite, and end product of glycolysis, has been studied for many uses, including its anti-inflammatory capabilities. Sodium pyruvate was recently shown by us to decrease inflammasome activation during IAV infection. Here, we investigated sodium pyruvate’s effects on IAVin vivo.We found that nebulizing mice with sodium pyruvate decreased morbidity and weight loss during infection. Additionally, treated mice consumed more chow during infection indicating improved symptoms. There were notable improvements in pro-inflammatory cytokine production (IL-1β) and lower virus titers on days 7 post-infection in mice treated with sodium pyruvate compared to control animals. As pyruvate acts on the host immune response and metabolic pathways and not directly on the virus, our data demonstrate that sodium pyruvate is a promising treatment option that is safe, effective, and unlikely to elicit antiviral resistance.
CaMKII activation triggers persistent formation and segregation of postsynaptic liquid phase
Authors: Hosokawa Tomohisa , Liu Pin-Wu , Cai Qixu , Ferreira Joana S. , Levet Florian , Butler Corey , Sibarita Jean-Baptiste , Choquet Daniel , Groc Laurent , Hosy Eric , Zhang Mingjie , Hayashi Yasunori
Published: November 2020

Transient information input to brain leads to persistent changes in synaptic circuit, thereby forming memory engrams. Synapse undergoes coordinated functional and structural changes during this process but how such changes are achieved by its component molecules still largely remain enigmatic. We found that activated CaMKII, the central player of synaptic plasticity, undergoes liquid-liquid phase separation (LLPS) with NMDAR subunit GluN2B. Due to CaMKII autophosphorylation, the condensate stably persists even after Ca2+is removed. The selective binding of activated CaMKII with GluN2B co-segregates AMPAR/neuroligin (NLGN) into a phase-in-phase assembly. Because postsynaptic NLGN clusters presynaptic neurexin and other active zone proteins thereby increasing the release probability of synaptic vesicles, this ensures efficient synaptic transmission. In this way, Ca2+-induced and persistent formation of LLPS by CaMKII serves as molecular basis of memory by functioning as an activity-dependent crosslinker for postsynaptic proteins and segregating trans-synaptic nanocolumns.
Bovine serum albumin as an immunogenic carrier facilitating the development of hapten-specific monoclonal antibodies
Authors: Zhao Ruotong , Jiang Mingjun
Published: November 2020

There is a common misconception that the generation of hapten-specific monoclonal antibodies (mAbs) requires the use of a heterologous conjugate to ensure carrier-specific antibodies not being detected. In this study, salbutamol (SAL) was used as a model hapten to exhibit the benefits of bovine serum albumin (BSA) as a carrier for developing hapten-specific mAbs. SAL-BSA conjugate would serve as both an immune antigen and a screening antigen during the preparation of SAL-specific mAbs. Six hybridomas were identified to secret mAbs specific for free SAL with minor or negligible cross-reactivity with other β-agonists. Meanwhile, none of hybrodomas secreting anti-BSA antibodies were screened out even though the fetal bovine serum (FBS) added to the medium decreased from 10% to 1% (v/v). Based on one of the six mAbs, 3F12, a direct competitive enzyme-linked immunosorbent assay (dcELISA) was developed for meausring SAL. Under the optimized assay, the quantitative working range was from 312.5 to 20,000 pg/mL (R2= 0.9959), with a limit of detection (LOD) of 142.9 pg/mL. The results showed that BSA is an efficient and suitable protein carrier for facilitating the development of hapten-specific mAbs.
Population genomics of the pathogenic yeast Candida tropicalis identifies hybrid isolates in environmental samples
Authors: O’Brien Caoimhe E. , Oliveira-Pacheco João , Cinnéide Eoin Ó , Hasse Max A. B. , Hittinger Chris Todd , Rogers Thomas R. , Zaragoza Oscar , Bond Ursula , Butler Geraldine
Published: November 2020

Candida tropicalis is a human pathogen that primarily infects the immunocompromised. Whereas the genome of one isolate, C. tropicalis MYA-3404, was originally sequenced in 2009, there have been no large-scale, multi-isolate studies of the genetic and phenotypic diversity of this species. Here, we used whole genome sequencing and phenotyping to characterize 77 isolates C. tropicalis isolates from clinical and environmental sources from a variety of locations. We show that most C. tropicalis isolates are diploids with approximately 2 - 6 heterozygous variants per kilobase. The genomes are relatively stable, with few aneuploidies. However, we identified one highly homozygous isolate and six isolates of C. tropicalis with much higher heterozygosity levels ranging from 36 - 49 heterozygous variants per kilobase. Our analyses show that the heterozygous isolates represent two different hybrid lineages, where the hybrids share one parent (A) with most other C. tropicalis isolates, but the second parent (B or C) differs by at least 4% at the genome level. Four of the sequenced isolates descend from an AB hybridization, and two from an AC hybridization. The hybrids are MTLa/α heterozygotes. Hybridization, or mating, between different parents is therefore common in the evolutionary history of C. tropicalis. The new hybrids were predominantly found in environmental niches, including from soil. Hybridization is therefore unlikely to be associated with virulence. In addition, we used genotype-phenotype correlation and CRISPR-Cas9 editing to identify a genome variant that results in the inability of one isolate to utilize certain branched-chain amino acids as a sole nitrogen source.

Author summary

Candida tropicalis is an important fungal pathogen, which is particularly common in the Asia-Pacific and Latin America. There is currently very little known about the diversity of genotype and phenotype of C. tropicalis isolates. By carrying out a phylogenomic analysis of 77 isolates, we find that C. tropicalis genomes range from very homozygous to highly heterozygous. We show that the heterozygous isolates are hybrids, most likely formed by mating between different parents. Unlike other Candida species, the hybrids are more common in environmental than in clinical niches, suggesting that for this species, hybridization is not associated with virulence. We also explore the range of phenotypes, and we identify a genomic variant that is required for growth on valine and isoleucine as sole nitrogen sources.
Pharyngeal pumping and tissue-specific transgenic P-glycoprotein expression influence macrocyclic lactone susceptibility inCaenorhabditis elegans
Authors: Gerhard Alexander P. , Krücken Jürgen , Neveu Cedric , Charvet Claude L. , Harmache Abdallah , von Samson-Himmelstjerna Georg
Published: November 2020

Macrocyclic lactone (ML) resistance has emerged in many parasitic nematodes including the pathogenic horse roundwormParascaris univalens. The underlying mechanism of ML resistance and the drug penetration routes into the nematodes remain to be elucidated. Drug efflux by P-glycoproteins is considered a potential resistance mechanism but conclusive functional evidence is lacking. To this end, we used a motility assay modified to stimulate pharyngeal pumping (PP) by bacteria or serotonin and tissue-specific expression ofPun-PGP-9 in the free-living model nematodeCaenorhabditis elegans. Here, stimulation of PP was identified as an important factor forC. elegansML susceptibility, increasing the EC50values of ivermectin by up to 11.1-fold and of moxidectin by 1.2-fold. In this context, intestinalPun-PGP-9 expression elicited a protective effect against ivermectin and moxidectin only in the presence of PP stimulation, increasing the EC50values by approximately 3- to 4-fold (ivermectin) or by < 1.3-fold (moxidectin). Conversely, epidermalPun-PGP-9 expression protected against moxidectin regardless of PP with EC50fold changes below 1.5 but against ivermectin with a considerable 2.9-fold EC50increase only when the drug is not actively ingested. Our results highlight the role of active drug ingestion by nematodes for susceptibility and provide conclusive functional evidence for a contribution of P-glycoproteins to ML resistance.

Author Summary

Parasitic nematode infections pose a serious threat to animal health, in particular in light of the widespread anthelmintic resistance in different nematode species. In equines, the roundwormParascaris univalensis a major pathogen of foals, exhibiting widespread resistance against macrocyclic lactones (MLs). This represents a particular challenge to animal health, but the underlying mechanisms and drug penetration routes remain mostly unknown. P-glycoprotein ABC-transporters have been linked to ML resistance in several parasitic nematodes. Here we demonstrate by tissue-specific overexpression ofPun-PGP-9 in the free-living model nematodeCaenorhabditis eleganstheir ability to reduce the susceptibility to two commonly used MLs, ivermectin and moxidectin. At the same time, active drug ingestion by pharyngeal pumping (PP) strongly enhanced ivermectin and moderately effects moxidectin susceptibility. In more detail, the effect of intestinal or epidermalPun-PGP-9 was dependent on active drug ingestion. These observations indicate differences in the drug penetration routes between ML derivatives and allow novel insight into the functional role of P-glycoproteins.
Pattern Recognition Receptor based Prognostic Biomarkers for predicting Survival of Uterine Corpus Endometrial Cancer Patients
Authors: Kaur Dilraj , Arora Chakit , Raghava G.P.S
Published: November 2020

In this study, we attempted to identify prognostic biomarkers for predicting survival risk of uterine corpus endometrial cancer (UCEC) patients from the gene expression profile of pattern recognition receptors (PRRs). A wide range of feature selection techniques have been tried, including network-based methods to identify a small number of genes from 331 PRR genes. Firstly, a risk stratification model has been developed using biomarker genes selected using a network-based approach and achieved HR=1.37 with p=0.294. Secondly, we developed a risk stratification model using biomarker of seven genes obtained from clustering and achieved HR=9.14 and p= 1.49×10-12. Finally, we developed various combinatorial models using biomarker of 15 PRR genes that were significantly associated with UCEC survival. We found that a multiple genes-based risk stratification model using nine genes (CLEC1B, CLEC3A, IRF7, CTSB, FCN1, RIPK2, NLRP10, NLRP9 and SARM1) gave the best result (HR=10.70, p=1.1×10-12, C=0.76, log-rank-p=8.15×10-14). The performance of this model improved significantly when we used the clinical stage of patients in combination with the expression of nine genes and achieved HR=15.23 (p=2.21×10-7, C=0.78, log-rank-p=2.76×10-17). We also developed classification models that can classify high-risk patients (survive ≤ 4.3 years) and low-risk patients (survive > 4.3 years) and achieved AUROC of 0.86. It was observed that specific genes are positively correlated with overall survival of UCEC patients. Based on these observations, we identified potential immunotherapeutic agents for treating UCEC patients.
Modelling optically pumped magnetometer interference as a mean (magnetic) field
Authors: Tierney Tim M , Alexander Nicholas , Mellor Stephanie , Holmes Niall , Seymour Robert , O’Neill George C , Maguire Eleanor A , Barnes Gareth R
Published: November 2020

Here we propose that much of the magnetic interference observed when using optically pumped magnetometers can be modeled spatially as a mean (magnetic) field. We show that this approximation reduces sensor level variability and substantially improves statistical power. This model does not require knowledge of the underlying neuroanatomy nor the sensor positions. It only needs information about the sensor orientation. Due to the model’s low rank there is little risk of removing substantial neural signal. However, we provide a framework to assess this risk for any sensor number, design or subject neuroanatomy. We find that the risk of unintentionally removing neural signal is reduced when multi-axis recordings are performed. We validated the method using a binaural auditory evoked response paradigm and demonstrated that the mean field correction increases reconstructed SNR in relevant brain regions in both the spatial and temporal domain. Considering the model’s simplicity and efficacy, we suggest that this mean field correction can be a powerful preprocessing step for arrays of optically pumped magnetometers.
An adaptive optics module for deep tissue multiphoton imaging in vivo
Authors: Rodríguez Cristina , Chen Anderson , Rivera José A. , Mohr Manuel A. , Liang Yajie , Sun Wenzhi , Milkie Daniel E. , Bifano Thomas G. , Chen Xiaoke , Ji Na
Published: November 2020

Understanding complex biological systems requires visualizing structures and processes deep within living organisms. We developed a compact adaptive optics module and incorporated it into two- and three-photon fluorescence microscopes, to measure and correct tissue-induced aberrations. We resolved synaptic structures in deep cortical and subcortical areas of the mouse brain, and demonstrated high-resolution imaging of neuronal structures and somatosensory-evoked calcium responses in the mouse spinal cord at unprecedented depths in vivo.
Identification of RNAs bound by Hfq reveals widespread RNA partners and a sporulation regulator in the human pathogenClostridioides difficile
Authors: Boudry Pierre , Piattelli Emma , Drouineau Emilie , Peltier Johann , Boutserin Anaïs , Lejars Maxence , Hajnsdorf Eliane , Monot Marc , Dupuy Bruno , Martin-Verstraete Isabelle , Gautheret Daniel , Toffano-Nioche Claire , Soutourina Olga
Published: November 2020

Noncoding RNAs (ncRNA) have emerged as important components of regulatory networks governing bacterial physiology and virulence. Previous deep-sequencing analysis identified a large diversity of ncRNAs in the human enteropathogenClostridioides (Clostridium) difficile.Some of them aretrans-encoded RNAs that could require the RNA chaperone protein Hfq for their action. Recent analysis suggested a pleiotropic role of Hfq inC. difficilewith the most pronounced effect on sporulation, a key process during the infectious cycle of this pathogen. However, a global view of RNAs interacting withC. difficileHfq is missing. In the present study, we performed RNA immunoprecipitation high-throughput sequencing (RIP-Seq) to identify Hfq-associated RNAs inC. difficile. Our work revealed a large set of Hfq-interacting mRNAs and ncRNAs, including mRNA leaders and coding regions, known and potential new ncRNAs. In addition totrans-encoded RNAs, new categories of Hfq ligands were found includingcis-antisense RNAs, riboswitches and CRISPR RNAs. ncRNA-mRNA and ncRNA-ncRNA pairings were postulated through computational predictions. Investigation of one of the Hfq-associated ncRNAs, RCd1, suggests that this RNA contributes to the control of late stages of sporulation inC. difficile. Altogether, these data provide essential molecular basis for further studies of post-transcriptional regulatory network in this enteropathogen.
The mutational landscape of human somatic and germline cells
Authors: Moore Luiza , Cagan Alex , Coorens Tim H.H. , Neville Matthew D.C. , Sanghvi Rashesh , Sanders Mathijs A. , Oliver Thomas R.W. , Leongamornlert Daniel , Ellis Peter , Noorani Ayesha , Mitchell Thomas J , Butler Timothy M. , Hooks Yvette , Warren Anne Y. , Jorgensen Mette , Dawson Kevin J. , Menzies Andrew , O’Neill Laura , Latimer Calli , Teng Mabel , van Boxtel Ruben , Iacobuzio-Donahue Christine A. , Martincorena Inigo , Heer Rakesh , Campbell Peter J. , Fitzgerald Rebecca C. , Stratton Michael R. , Rahbari Raheleh
Published: November 2020

During the course of a lifetime normal human cells accumulate mutations. Here, using multiple samples from the same individuals we compared the mutational landscape in 29 anatomical structures from soma and the germline. Two ubiquitous mutational signatures, SBS1 and SBS5/40, accounted for the majority of acquired mutations in most cell types but their absolute and relative contributions varied substantially. SBS18, potentially reflecting oxidative damage, and several additional signatures attributed to exogenous and endogenous exposures contributed mutations to subsets of cell types. The mutation rate was lowest in spermatogonia, the stem cell from which sperm are generated and from which most genetic variation in the human population is thought to originate. This was due to low rates of ubiquitous mutation processes and may be partially attributable to a low cell division rate of basal spermatogonia. The results provide important insights into how mutational processes affect the soma and germline.
Binding Dynamics of Disordered Linker Histone H1 with a Nucleosomal Particle
Authors: Wu Hao , Dalal Yamini , Papoian Garegin A.
Published: November 2020

Linker histone H1 is an essential regulatory protein for many critical biological processes, such as eukaryotic chromatin packaging and gene expression. Mis-regulation of H1s is commonly observed in tumor cells, where the balance between different H1 subtypes has been shown to alter the cancer phenotype. Consisting of a rigid globular domain and two highly charged terminal domains, H1 can bind to multiple sites on a nucleosomal particle to alter chromatin hierarchical condensation levels. In particular, the disordered H1 amino- and carboxyl-terminal domains (NTD/CTD) are believed to enhance this binding affinity, but their detailed dynamics and functions remain unclear. In this work, we used a coarse-grained computational model AWSEM-DNA to simulate the H1.0b-nucleosome complex, namely chromatosome. Our results demonstrate that H1 disordered domains restrict the dynamics of both globular H1 and linker DNA arms, resulting in a more compact and rigid chromatosome particle. Furthermore, we identified regions of H1 disordered domains that are tightly tethered to DNA near the entry-exit site. Overall, our study elucidates at near atomic resolution the way the disordered linker histone H1 modulates nucleosome’s structural preferences and conformational dynamics.
Single molecule tracking and analysis framework including theory-predicted parameter settings
Authors: Kuhn Timo , Hettich Johannes , Gebhardt J. Christof M.
Published: November 2020

Imaging, tracking and analyzing individual biomolecules in living systems is a powerful technology to obtain quantitative kinetic and spatial information such as reaction rates, diffusion coefficients and localization maps. Common tracking tools often operate on single movies and require additional manual steps to analyze whole data sets or to compare different experimental conditions. We report a fast and comprehensive single molecule tracking and analysis framework (TrackIt) to simultaneously process several multi-movie data sets. A user-friendly GUI offers convenient tracking visualization, multiple state-of-the-art analysis procedures, display of results, and data im- and export at different levels to utilize external software tools. We applied our framework to quantify dissociation rates of a transcription factor in the nucleus and found that tracking errors, similar to fluorophore photobleaching, have to be considered for reliable analysis. Accordingly, we developed an algorithm, which accounts for both tracking losses and suggests optimized tracking parameters when evaluating reaction rates. Our versatile and extensible framework facilitates quantitative analysis of single molecule experiments at different experimental conditions.
Factors Underlying Asymmetric Dynamics of Disaggregase and Microtubule Severing AAA+ Machines
Authors: Damre Mangesh , Dayananda Ashan , Varikoti Rohith Anand , Stan George , Dima Ruxandra I.
Published: November 2020

Disaggregation and microtubule-severing nanomachines from the AAA+ (ATPases associated with various cellular activities) superfamily assemble into ring–shaped hexamers that enable protein remodeling by coupling large–scale conformational changes with application of mechanical forces within a central pore by loops protruding within the pore. We probed these motions and intra-ring interactions that support them by performing extensive explicit solvent molecular dynamics simulations of single-ring severing proteins and the double-ring disaggregase ClpB. Simulations reveal that dynamic stability of hexamers of severing proteins and of the nucleotide binding domain 1 (NBD1) ring of ClpB, which belong to the same clade, involves a network of salt bridges that connect conserved motifs of central PL1 loops of the hexamer. Clustering analysis of ClpB highlights correlated motions of domains of neighboring protomers supporting strong inter-protomer collaboration. Severing proteins have weaker inter-protomer coupling and stronger intra-protomer stabilization through salt bridges formed between PL2 and PL3 loops. Distinct mechanisms are identified in the NBD2 ring of ClpB involving weaker inter–protomer coupling through salt bridges formed by non–canonical loops and stronger intra–protomer coupling. Pore width fluctuations associated with the PL1 constriction in the spiral states, in the presence of a substrate peptide, highlight stark differences between narrowing of channels of severing proteins and widening of the NBD1 ring of ClpB. This indicates divergent substrate processing mechanisms of remodeling and translocation by ClpB and substrate tail-end gripping and possible wedging on microtubule lattice by severing enzymes. Relaxation dynamics of the distance between the PL1 loops and the centers of mass of protomers reveals observation-time-dependent dynamics, leading to predicted relaxation times of tens of microseconds on millisecond experimental timescales. For ClpB the predicted relaxation time is in excellent agreement with the extracted time from smFRET experiments.
SARS-CoV-2 utilizes a multipronged strategy to suppress host protein synthesis
Authors: Finkel Yaara , Gluck Avi , Winkler Roni , Nachshon Aharon , Mizrahi Orel , Lubelsky Yoav , Zuckerman Binyamin , Slobodin Boris , Yahalom-Ronen Yfat , Tamir Hadas , Ulitsky Igor , Israely Tomer , Paran Nir , Schwartz Michal , Stern-Ginossar Noam
Published: November 2020

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of the ongoing coronavirus disease 19 (COVID-19) pandemic. Despite the urgent need, we still do not fully understand the molecular basis of SARS-CoV-2 pathogenesis and its ability to antagonize innate immune responses. Here, we use RNA-sequencing and ribosome profiling along SARS-CoV-2 infection and comprehensively define the mechanisms that are utilized by SARS-CoV-2 to shutoff cellular protein synthesis. We show SARS-CoV-2 infection leads to a global reduction in translation but that viral transcripts are not preferentially translated. Instead, we reveal that infection leads to accelerated degradation of cytosolic cellular mRNAs which facilitates viral takeover of the mRNA pool in infected cells. Moreover, we show that the translation of transcripts whose expression is induced in response to infection, including innate immune genes, is impaired, implying infection prevents newly transcribed cellular mRNAs from accessing the ribosomes. Overall, our results uncover the multipronged strategy employed by SARS-CoV-2 to commandeer the translation machinery and to suppress host defenses.
Intracellular localisation ofMycobacterium tuberculosisaffects antibiotic efficacy
Authors: Santucci Pierre , Greenwood Daniel J. , Fearns Antony , Chen Kai , Jiang Haibo , Gutierrez Maximiliano G.
Published: November 2020

To be effective, chemotherapy against tuberculosis (TB) must kill the intracellular population ofMycobacterium tuberculosis(Mtb). However, how host cell environments affect antibiotic accumulation and efficacy remains elusive. Pyrazinamide (PZA) is a key antibiotic against TB, yet its behaviour is not fully understood. Here, by using correlative light, electron, and ion microscopy to image PZA at the subcellular level, we investigated how human macrophage environments affect PZA activity. We discovered that PZA accumulates heterogeneously between individual bacteria in multiple host cell environments. Crucially, Mtb phagosomal localisation and acidification increase PZA accumulation and efficacy. By imaging two antibiotics commonly used in combined TB therapy, we showed that bedaquiline (BDQ) significantly enhances PZA accumulation by a host cell mediated mechanism. Thus, intracellular localisation and specific microenvironments affect PZA accumulation and efficacy; explaining the potentin vivoefficacy compared to its modestin vitroactivity and the critical contribution to TB combination chemotherapy.
RNA 3D modeling with FARFAR2, online
Authors: Watkins Andrew , Das Rhiju
Published: November 2020

Understanding the three-dimensional structure of an RNA molecule is often essential to understanding its function. Sampling algorithms and energy functions for RNA structure prediction are improving, due to the increasing diversity of structural data available for training statistical potentials and testing structural data, along with a steady supply of blind challenges through the RNA Puzzles initiative. The recent FARFAR2 algorithm enables near-native structure predictions on fairly complex RNA structures, including automated selection of final candidate models and estimation of model accuracy. Here, we describe the use of a publicly available webserver for RNA modeling for realistic scenarios using FARFAR2, available at https://rosie.rosettacommons.org/farfar2. We walk through two cases in some detail: a simple model pseudoknot from the frameshifting element of beet western yellows virus modeled using the “basic interface” to the webserver, and a replication of RNA-Puzzle 20, a metagenomic twister sister ribozyme, using the “advanced interface.” We also describe example runs of FARFAR2 modeling including two kinds of experimental data: a c-di-GMP riboswitch modeled with low resolution restraints from MOHCA-seq experiments and a tandem GA motif modeled with 1H NMR chemical shifts.
Frontoparietal, cerebellum network codes for accurate intention prediction in altered perceptual conditions
Authors: Ceravolo L. , Schaerlaeken S. , Frühholz S. , Glowinski D. , Grandjean D.
Published: November 2020

Integrating and predicting intentions and actions of others are crucial components of social interactions, but the behavioral and neural underpinnings of such mechanisms in altered perceptual conditions remain poorly understood. We demonstrated that expertise was necessary to successfully understand and evaluate communicative intent in spatially and temporally altered visual representations of music plays, recruiting frontoparietal regions and several sub-areas of the cerebellum. Functional connectivity between these brain areas revealed widespread organization, especially in the cerebellum. This network may be essential to assess communicative intent in ambiguous or complex visual scenes.
Semi-empirical model to estimate ideal conditions for the growth of large protein crystals
Authors: Nakamura Hirohiko , Takahashi Sachiko , Inaka Koji , Tanaka Hiroaki
Published: November 2020

A large high-quality crystal is required to specify the positions of H atoms in neutron structural analysis. Consequently, several methods have been proposed for obtaining such large crystals, and theoretical considerations for growing them have been presented. However, further investigation is required to obtain a numerical model that can provide quantitative experimental conditions for obtaining a single large crystal. In the case of protein crystallization experiments, the amount of sample is often limited. Therefore, it is more realistic to make a rough estimation from a small number of experiments. This paper proposes a method of estimating the optimum experimental conditions for the growth of large protein crystals by performing a small number of experiments using a micro-batch method and reporting a numerical model based on nucleation theory and a linear approximation of the crystal-growth rate. Specifically, micro-batch experiments are performed to provide the empirical parameters for the model and to help to estimate the conditions for the growth of a crystal of a predetermined size using a certain sample concentration and volume. This method is offered as a step on the path towards efficiently and rationally producing large crystals that can be subjected to neutron diffraction without depending on luck or on performing many experiments. It is expected to contribute to drug design and the elucidation of protein molecular functions and mechanisms by obtaining positional information on H atoms in the protein molecule, which is an advantage of neutron diffraction.
Assessing nitrogen dioxide (NO2) impact on health pre- and post-COVID-19 pandemic using IoT in India
Authors: R. Sitharthan , D. Shanmuga Sundar , M. Rajesh , Madurakavi Karthikeyan , I. Jacob Raglend , J. Belwin Edward , R. Raja Singh , R. Kumar
Published: November 2020

Purpose

Corona Virus Disease 2019 (COVID-19) is a deadly virus named after severe acute respiratory syndrome coronavirus 2; it affects the respiratory system of the human and sometimes leads to death. The COVID-19 mainly attacks the person with previous lung diseases; the major cause of lung diseases is the exposure to nitrogen dioxide (NO2) for a longer duration. NO2 is a gaseous air pollutant caused as an outcome of the vehicles, industrial smoke and other combustion processes. Exposure of NO2 for long-term leads to the risk of respiratory and cardiovascular diseases and sometimes leads to fatality. This paper aims to analyze the NO2 level impact in India during pre- and post-COVID-19 lockdown. The study also examines the relationship between the fatality rate of humans because of exposure to NO2 and COVID-19.

Design/methodology/approach

Spatial analysis has been conducted in India based on the mortality rate caused by the COVID-19 using the data obtained through Internet of Medical things. Meanwhile, the mortality rate because of the exposure of NO2 has been conducted in India to analyze the relationship. Further, NO2 level assessment is carried out using Copernicus Sentinel-5P satellite data. Moreover, aerosol optical depth analysis has been carried out based on NASA’s Earth Observing System data.

Findings

The results indicate that NO2 level has dropped 20-year low because of the COVID-19 lockdown. The results also determine that the mortality rate because of long-time exposure to NO2 is higher than COVID-19 and the mortality rate because of COVID-19 may be a circumlocutory effect owing to the inhalation of NO2.

Originality/value

Using the proposed approach, the COVID-19 spread can be identified by knowing the air pollution in major cities. The research also identifies that COVID-19 may have an effect because of the inhalation of NO2, which can severe the COVID-19 in the human body.
Customer relationship management and patient satisfaction and loyalty in selected hospitals in Ghana
Authors: Abekah-Nkrumah Gordon , Yaa Antwi Maame , Braimah Stephen Mahama , Ofori Charles Gyamfi
Published: November 2020

Purpose

This paper aims to examine the effect of customer relationship management (CRM) on patient satisfaction and patient loyalty, controlling for other socio-demographic characteristics.

Design/methodology/approach

The study used a two-stage sampling process and structured questionnaires to collect data from 788 patients from three health facilities (public, quasi-public and private) in Greater Accra, Ghana. The data collected was analyzed using descriptive statistics and regression via the partial least squares-based structural equation model.

Findings

The results suggest that CRM is significantly positively correlated with patient satisfaction and patient loyalty, with patient satisfaction also significantly correlated with patient loyalty. Additionally, the results suggest that the introduction of education, health facility ownership, health insurance status and gender, neither impact significantly on the relationship between CRM and patient satisfaction/patient loyalty nor influenced patient satisfaction and patient loyalty directly.

Research limitations/implications

The findings of the current paper can have substantial practice implications for operators in the health-care industry in Ghana. CRM components such as service quality, customer service, communication and the use of appropriate technology to deliver service will be fundamental if organizations operating in the health-care ecosystem in Ghana are to be able to compete effectively.

Originality/value

This is one of the very few papers on the relationship between CRM and patient satisfaction and patient loyalty in African health-care literature. Thus, the findings of the paper can constitute a great resource not only to academics but also to practitioners who are looking to be competitive in the health-care market.
Retail 4.0 adoption and firm performance among Malaysian retailers: the role of enterprise risk management as moderator
Authors: Sakrabani Poorni , Teoh Ai Ping
Published: November 2020

Purpose

The purpose of this study was to ascertain the determinants of firm performance for Malaysian retailers.

Design/methodology/approach

An online survey was conducted to collect responses from members of the Malaysian Retailers' Chain Association. A total of 126 responses were obtained. Data analysis was done by using the PLS-SEM method.

Findings

The results of the study indicate that Retail 4.0 adoption is able to improve retailers' performance as-a-whole by improving the four perspectives of firm performance as given in the Balanced Scorecard, i.e. the finance perspective, the customer perspective, the internal processes' perspective and also learning and growth perspective. Further, enterprise risk management was found to have a positive moderating effect on retailers' performance as-a-whole and also on the finance and customer perspectives of performance.

Research limitations/implications

The study was conducted only in Malaysia and so, it might be geographically limited. Besides, it is cross-sectional in nature and therefore, the impact might be different if the study had been conducted over a longer period.

Practical implications

This study provides a useful framework for retailers who are seeking to improve firm performance.

Originality/value

This is one of the first studies to show the impact of Retail 4.0 adoption on firm performance. Besides, this is also the first time, enterprise risk management has been introduced as a positive moderator on the impact of technology adoption on retailers' performance.
Exploring young consumer's decision‐making for luxury co-branding combinations
Authors: Yu Yanan , Rothenberg Lori , Moore Marguerite
Published: November 2020

Purpose

The purpose of this paper is to identify the realistic trade-offs young consumers make when evaluating luxury co-branding combinations based on signalling theory.

Design/methodology/approach

Conjoint analysis was employed to evaluate the relative impact of four major attributes (i.e. brand combinations, retail channels, uniqueness and price) on consumer desirability for luxury co-branding combinations. The data were analysed using desirability indices.

Findings

Brand combinations, uniqueness and price significantly impact consumer desirability of luxury co-branding combinations. The luxury brand and sportswear combination results in the highest desirability when price is more similar to the sportswear constituent and participants perceive that the collaboration as exclusive.

Practical implications

The results suggest that luxury brands need to consider the partnering brand's retail format primarily for co-branding strategy. Luxury brand collaborations with sportswear and premium priced streetwear brands are more likely to result in higher desirability among consumers compared to collaborations with fast fashion and mass-market brands. Additionally, uniqueness may not be effective as a point of differentiation in cases where luxury brands cannot guarantee a single yearly collaboration.

Originality/value

The decision to use existing brands for the fictitious combinations developed more sensible scenarios for respondents. In addition, rather than discrete questions, attribute-based combinations provide a more realistic depiction of consumers' decision making on luxury co-branding. Finally, the results provide marketing practitioners with practical directions for future development of fashion luxury co-branding strategy.
An uncertain, erratic story: the pandemic in the UK
Authors: Lapsley Irvine
Published: November 2020

Purpose

The purpose of this paper is to study the pandemic from the perspective of the UK health-care system and risk management.

Design/methodology/approach

This paper follows a storytelling perspective. The author reflects on his experiences through the lens of research on health care and risk management.

Findings

The impact of the pandemic has been so massive that it has challenged the capacity of the UKs National Health Service. The political influences at work have not always promoted best practice in risk management and indicate blame-avoidance strategies by politicians.

Research limitations/implications

A single country experience of COVID-19.

Practical implications

There are major issues of asset management, of delays in decision-making, of supply chain problems and the need to reform processes of handling of crisis management.

Originality/value

This is an individual account of experiences of the pandemic.
Pandemic policy making: the health and wellbeing effects of the cessation of volunteering on older adults during the COVID-19 pandemic
Authors: Grotz Jurgen , Dyson Sally , Birt Linda
Published: November 2020

Purpose

This policy-orientated commentary aims to provide a perspective on the effects of policy changes designed to reduce the risk of infection as a result of COVID-19. The example of the abrupt cessation of volunteering activities is used to consider the policy and practice implications that need to be acknowledged in new public service research to deal with the on-going implications of the COVID-19 pandemic and for future preparedness.

Design/methodology/approach

The paper will provide a critical challenge to English pandemic health policy making, in particular, the national instruction “to stop non-essential contact with others” without a strategy on how to remedy the serious side effects of this instruction, in particular on older adults.

Findings

The abrupt cessation of volunteering activities of and for older people because of the COVID-19 pandemic is highly likely to have negative health and wellbeing effects on older adults with long-term and far-reaching policy implications.

Originality/value

The paper combines existing knowledge volunteering of and for older adults with early pandemic practice evidence to situate an emerging health and wellbeing crisis for older adults. It emphasises the importance of immediate further detailed research to provide evidence for policy and practice following the lifting of COVID-19 related restrictions and in preparation for future crises.
Talent management after an acquisition: a case study of Roche and Genentech
Authors: Béraud Mathilde , Drajac Carole , Thomas Mark
Published: November 2020

Purpose

As the pharmaceutical industry faces a more changing environment, talent management appears to be a key differentiating element. Key talent retention strategies must be assessed during the mergers and acquisitions negotiations and implemented during post-acquisition integration. The purpose of this paper is to show how this can be done.

Design/methodology/approach

The paper adopts a single-case approach to show how talent can be managed during the post-acquisition phase after a takeover. Focussing on the acquisition of Genentech by Roche in 2009, it demonstrates how the Swiss pharmaceutical giant overcame a difficult initial start to the acquisition by adopting a nuanced talent management strategy.

Findings

The findings from this paper demonstrate best practice management and retention strategies needed to retain key talent. A decade after the acquisition, the Roche–Genentech tie-up is cited as one of the most successful in the life sciences industry. Roche’s talent management strategy has gained particular applause with Genentech consistently being named one of the best places to work (Wharton Work/Life, 2016). Investors are equally content. Sales of Genentech’s main products have tripled to $21bn since the acquisition.

Originality/value

This paper offers a concise and clear outline of the HR strategies used by Roche to ensure the successful integration of Genentech. During the takeover, talent management issues had the potential to be particularly acute given the highly independent DNA of Genentech’s organisation structure. As the pharmaceutical industry faces a more changing environment, efficient talent management appears to be a key differentiating element.
Sensitivity of polyphagous (Plodia interpunctella) and stenophagous (Ephestia kuehniella) storage moths to residual insecticides: effect of formulation and larval age
Authors: Stejskal Vaclav , Stara Jitka , Pekar Stano , Nesvorna Marta , Hubert Jan
Published: November 2020

Pyralid moths, Ephestia kuehniella and Plodia interpunctella, are prevalent stored product pests. The insecticides are the main tool to control these moths in the stores. The data describing the response of these moths to insecticides are scarce. The lethal effect of the organophosphate, pyrethroid, and halogenated‐pyrrole on moths larvae were compared in laboratory test. The hypothesis was that the very polyphagous P. interpunctella would have generally higher insecticide tolerance than that of the stenophagous E. kuehniella. Different insecticide concentrations were applied onto the inner surface of glass tube vials. Ten larvae of 14 or 21 d old of E. kuehniella and 7 or 14 d old of P. interpunctella were used by treatment. The larval mortality was checked after 24 h of exposure. The mortality was significantly influenced by age of larvae and the groups of chemicals. No differences among the efficacies of the tested formulations with identical active compounds were found, except significant different mortality of E. kuehniella on deltamethrin formulations. A comparison of analytical standards showed that P. interpunctella was less susceptible to the active ingredient pirimiphos‐methyl than E. kuehniella, while E. kuehniella was less susceptible to deltamethrin than P. interpunctella. No differences between the two species were observed for chlorfenapyr. We therefore rejected the hypothesis that polyphagy/stenophagy can be a general predictor of insecticide tolerance in the two tested storage moths. The most important finding for effective use was that the young larvae of both species were more susceptible to tested insecticides than older larvae.
Potential of laser‐induced fluorescence‐light detection and ranging for future stand‐off virus surveillance
Authors: Owoicho Oloche , Olwal Charles Ochieng’ , Quaye Osbourne
Published: November 2020

Viruses remain a significant public health concern worldwide. Recently, humanity has faced deadly viral infections, including Zika, Ebola and the current severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2). The threat is associated with the ability of the viruses to mutate frequently and adapt to different hosts. Thus, there is the need for robust detection and classification of emerging virus strains to ensure that humanity is prepared in terms of vaccine and drug developments. A point or stand‐off biosensor that can detect and classify viruses from indoor and outdoor environments would be suited for viral surveillance. Light detection and ranging (LiDAR) is a facile and versatile tool that has been explored for stand‐off detection in different environments including atmospheric, oceans and forest sensing. Notably, laser‐induced fluorescence‐light detection and ranging (LIF‐LiDAR) has been used to identify MS2 bacteriophage on artificially contaminated surgical equipment or released amidst other primary biological aerosol particles in laboratory‐like close chamber. It has also been shown to distinguish between different picornaviruses. Currently, the potentials of the LIF‐LiDAR technology for real‐time stand‐off surveillance of pathogenic viruses in indoor and outdoor environments have not been assessed. Considering the increasing applications of LIF‐LiDAR for potential microbial pathogens detection and classification, and the need for more robust tools for viral surveillance at safe distance, we critically evaluate the prospects and challenges of LIF‐LiDAR technology for real‐time stand‐off detection and classification of potentially pathogenic viruses in various environments.