bluuebunny/crossref_metadata_2025_split huggingface dataset:
Adaptation to DNA damage as a bet-hedging mechanism in a fluctuating environment
Authors: Roux Pierre , Salort Delphine , Xu Zhou 
Published: March 2021

AbstractIn response to DNA damage, efficient repair is essential for cell survival and genome integrity. In eukaryotes, the DNA damage checkpoint is a signalling pathway that coordinates this response and arrests the cell cycle to provide time for repair. However, when repair fails or when the damage is not repairable, cells can eventually bypass the DNA damage checkpoint and undergo cell division despite persistent damage, a process called adaptation to DNA damage. Interestingly, adaptation occurs with a delayed timing compared to repair and shows a large variation in time, two properties that may provide a survival advantage at the population level without interfering with repair. Here, we explore this idea by mathematically modelling cell survival in response to DNA damage and focusing on adaptation parameters. We find that the delayed adaptation timing indeed maximizes survival, but its heterogeneity is beneficial only in a fluctuating damage-inducing environment. Finally, we show that adaptation does not only contribute to survival but also to genome instability and mutations, which might represent another criterion for its selection through-out evolution. Overall, we propose that adaptation can act as a bet-hedging mechanism for cell survival in response to DNA damage.
Single-molecule conformational dynamics of a transcription factor reveals a continuum of binding modes controlling association and dissociation
Authors: Chen Wei , Lu Wei , Wolynes Peter G. , Komives Elizabeth A. 
Published: March 2021

AbstractBinding and unbinding of transcription factors to DNA are kinetically controlled to regulate the transcriptional outcome. Control of the release of the transcription factor NF-κB from DNA is achieved through accelerated dissociation by the inhibitor protein IκBα. Using single-molecule FRET, we observe a continuum of conformations of NF-κB in free and DNA-bound states interconverting on the subseconds to minutes timescale, comparable toin vivobinding on the seconds timescale, suggesting that structural dynamics directly control binding kinetics. Much of the DNA-bound NF-κB is partially bound, allowing IκBα invasion to facilitate DNA dissociation. IκBα induces a locked conformation where the DNA-binding domains of NF-κB are too far apart to bind DNA, whereas the loss-of-function IκBα mutant retains the NF-κB conformational ensemble. Overall, our results suggest a novel mechanism with a continuum of binding modes for controlling association and dissociation of transcription factors.
The phytonutrient cinnamaldehyde limits intestinal inflammation and enteric parasite infection
Authors: Zhu Ling , Andersen-Civil Audrey I.S. , Myhill Laura J. , Thamsborg Stig M. , Kot Witold , Krych Lukasz , Nielsen Dennis S. , Blanchard Alexandra , Williams Andrew R. 
Published: March 2021

AbstractPhytonutrients such as cinnamaldehyde (CA) have been studied for their effects on metabolic diseases, but their influence on mucosal inflammation and immunity to enteric infection are not well documented. Here, we show that consumption of CA significantly down-regulates transcriptional pathways connected to inflammation in the small intestine of mice. During infection with the enteric helminth Heligomosomoides polygyrus, CA-treated mice displayed higher growth rates and less worms, concomitant with altered T-cell populations in mesenteric lymph nodes. Furthermore, infection-induced changes in gene pathways connected to cell cycle and mitotic activity were counteracted by CA. Mechanically, CA did not appear to exert activity through a prebiotic effect, as CA treatment did not significantly change the composition of the gut microbiota. Instead, in vitro experiments showed that CA directly induced xenobiotic metabolizing pathways in intestinal epithelial cells and suppressed endotoxin-induced inflammatory responses in macrophages. Thus, CA down-regulates inflammatory pathways in the intestinal mucosa and regulates host responses to enteric infection. These properties appear to be largely independent of the gut microbiota and instead connected to CA’s ability to induce antioxidant pathways in intestinal cells. Our results encourage further investigation into the use of CA and related phytonutrients as functional food components to promote intestinal health in humans and animals.
Structural basis of LhcbM5-mediated state transitions in green algae
Authors: Pan Xiaowei , Tokutsu Ryutaro , Li Anjie , Takizawa Kenji , Song Chihong , Murata Kazuyoshi , Yamasaki Tomohito , Liu Zhenfeng , Minagawa Jun , Li Mei 
Published: March 2021

AbstractIn green algae and plants, state transitions serve as a short-term light acclimation process to regulate light harvesting capacity of photosystems I and II (PSI and PSII). During the process, a portion of the light-harvesting complexes II (LHCII) are phosphorylated, dissociate from PSII and bind PSI to form PSI-LHCI-LHCII supercomplex. Here we report high-resolution structures of PSI-LHCI-LHCII supercomplex fromChlamydomonas reinhardtii, revealing the mechanism of assembly between PSI-LHCI complex and two phosphorylated LHCII trimers containing all four types of LhcbM proteins. Two specific LhcbM isoforms, namely LhcbM1 and LhcbM5, directly interact with the PSI core through their phosphorylated amino-terminal regions. Furthermore, biochemical and functional studies on mutant strains lacking either LhcbM1 or LhcbM5 indicate that only LhcbM5 is indispensable in the supercomplex formation. The results unraveled the specific interactions and potential excitation energy transfer routes between green algal PSI and two phosphorylated LHCIIs.
Ribosomal RNA methylation by GidB modulates discrimination of mischarged tRNA
Authors: Bi Zhuo , Chen Yu-Xiang , Young Iris D. , Su Hong-Wei , Chen Yuemeng , Hong Jia-Yao , Fraser James S. , Javid Babak 
Published: March 2021

SummaryDespite redundant cellular pathways to minimize translational errors, errors in protein synthesis are common. Pathways and mechanisms to minimize errors are classified as pre-ribosomal or ribosomal. Pre-ribosomal pathways are primarily concerned with the appropriate charging of tRNAs with their cognate amino acid. By contrast, the ribosomal decoding centre is considered ‘blind’ to mischarged tRNAs since these have cognate codon•anti-codon pairing. Here, we identified that in mycobacteria, deletion of the 16S ribosomal RNA methyltransferase gidB led to increased ribosomal discrimination of mischarged tRNAs. Discrimination only occurred in mycobacteria enriched from environments or genetic backgrounds with high rates of mistranslation. GidB deletion was necessary but not sufficient for reducing mistranslation due to misacylation. Analysis of new cryoEM structures of the M. smegmatis ribosomes derived from wild-type and gidB-deleted strains point to the interaction between the base methylated by GidB on the 16S RNA and an asparagine on the ribosomal S12 protein that when mistranslated to aspartate may be involved in altering translational fidelity. Our data suggest a mechanism by which mycobacterial ribosomes can discriminate mischarged tRNAs and that 16S rRNA differential methylation by GidB may act to prevent catastrophic translational error.
Targeting Biofilm of MDRProvidencia stuartiiby Phages Using a Catheter Model
Authors: Rakov Chani , Porat Shira Ben , Alkalay-Oren Sivan , Yerushalmy Ortal , Abdalrhman Mohanad , Gronovich Niv , Huang Lina , Pride David , Coppenhagen-Glazer Shunit , Nir-Paz Ran , Hazan Ronen 
Published: March 2021

AbstractProvidencia spp. are emerging pathogens mainly in nosocomial infections.Providencia stuartiiin particular is involved in urinary tract infections and contributes significantly to the high incidence of biofilm-formation in catheterized patients. Furthermore, recent reports suggested a role for multiple drug resistant (MDR)P. stuartiiin hospital-associated outbreaks which leads to excessive complications resulting in challenging treatments. Phage therapy is currently one of the most promising solutions to combat antibiotic-resistant infections. However, the number of available phages targetingProvidencia spp. is extremely limited, restricting the use of phage therapy in such cases. In the present study, we describe the isolation and characterization of 17 lytic and lysogenic bacteriophages targeting clinical isolates ofProvidencia spp. as part of the Israeli Phage Bank (IPB). These phages, isolated from sewage samples, were evaluated for host range activity and effectively eradicated 95% of the tested bacterial strains isolated from different geographic locations and displaying a wide range of antibiotic resistance. Their lytic activity is demonstrated on agar plates, planktonic cultures, and biofilm formed in a catheter model. The results suggest that these bacteriophages can potentially be used for treatment of antibiotic-resistantProvidencia spp. infections in general and of urinary tract infections in particular.
Upper respiratory tract SARS-CoV-2 RNA loads in symptomatic and asymptomatic children and adults
Authors: Costa Rosa , Bueno Felipe , Albert Eliseo , Torres Ignacio , Carbonell-Sahuquillo Silvia , Barrés-Fernández Ana , Sánchez David , Padrón Carmelo , Colomina Javier , Lázaro Carreño María Isabel , Bretón-Martínez José Rafael , Martínez-Costa Cecilia , Navarro David 
Published: March 2021

ABSTRACTObjectivesThere is limited information comparing SARS-CoV-2 RNA load in the upper respiratory tract (URT) between children and adults, either presenting with COVID-19 or asymptomatic. Here we conducted a retrospective, single center study involving a large cohort of SARS-CoV-2 infected individuals to address this issue.Patients and MethodsA total of 1,184 consecutive subjects (256 children and 928 adults) testing positive for SARS-COV-2 RNA in nasopharyngeal exudates (NP) were included, of whom 424 (121 children and 303 adults) had COVID-19 not requiring hospitalization and 760 (135 children and 625 adults) were asymptomatic close contacts of COVID-19 patients. SARS-CoV-2 RNA testing was carried out using the TaqPath COVID-19 Combo Kit (Thermo Fisher Scientific, MS, USA). The AMPLIRUN® TOTAL SARS-CoV-2 RNA Control (Vircell SA, Granada, Spain) was used for estimating SARS-CoV-2 RNA loads (in copies/mL).ResultsMedian SARS-COV-2 RNA loads were comparable between adults and children with COVID-19 (7.14 log10 copies/ml vs. 6.98 log10 copies/ml; P=0.094). Median SARS-CoV-2 RNA load in asymptomatic children and adults was similar (6.20 log10 copies/ml vs. 6.48 log10 copies/ml; P=0.97). Children with COVID-19 symptoms displayed SARS-CoV-2 RNA loads comparable to their asymptomatic counterparts (P=0.61). Meanwhile in adults, median SARS-CoV-2 RNA load was significantly higher in symptomatic than in asymptomatic subjects (P=<0.001), yet comparable (P=0.61) when the analysis excluded patients sampled within 48 h after symptoms onset.ConclusionsThe data suggest that children may be drivers of SARS-CoV-2 transmission in the general population at the same level as adults.
Heritage hotels and customer experience: a text mining analysis of online reviews
Authors: Chittiprolu Vinay , Samala Nagaraj , Bellamkonda Raja Shekhar 
Published: March 2021

PurposeIn business, online reviews have an economic impact on firm performance. Customers’ data in the form of online reviews was used to understand the appreciation and service complaints written by previous customers. The study is an analysis of the online reviews written by the customers about Indian heritage hotels. This study aims to understand the dimensions of service appreciation and service complaints by comparing positive- and negative-rated reviews and find the patterns in the determinants of the satisfaction and dissatisfaction of the customers.Design/methodology/approachA total of 23,643 online reviews about heritage hotels were collected from the TripAdvisor website by using a Web crawler developed in Python. A total of 1000 reviews were randomly selected for further analysis to eliminate the bandwagon effect. Unsupervised text mining techniques were used to analyze reviews and find out the interesting patterns in text data.FindingsBased on Herzberg two-factor theory, this study found satisfied and dissatisfied determinants separately. The study revealed some common categories discussed by satisfied and dissatisfied customers. The factors which satisfy the customers may also dissatisfy the customers if not delivered properly. Satisfied customers mentioned about tangible features of the hotel stay, which includes physical signifiers, traditional services, staff behavior and professionalism and core products (rooms, food). However, most of the customers complained about intangible service problems, such as staff attitude, services failure, issues with reservation and food, value for money and room condition. The results are contradicting with commercial hotels-based studies owing to the unique services provided by heritage hotels.Practical implicationsThe dimensions for satisfaction and dissatisfaction among customer of heritage hotels provide marketers to understand the real emotion and perception of the customers. As these dimensions were extracted through text mining of the reviews written by the customer of heritage hotels, the results would certainly give better insights to the hotel marketers.Originality/valueThe study is a rare attempt to study online reviews of customers on heritage hotels through a text mining approach and find the patterns in the behavior and the determinants of satisfaction and dissatisfaction of customers.
“Exotic, welcoming and fresh”: stereotypes in new Nordic branding
Authors: Lerøy Sataøen Hogne 
Published: March 2021

PurposeIdeas related to “the Nordic” are important in the reconstruction of national identities in Denmark, Finland, Iceland, Norway and Sweden, and these countries’ modern national narratives are structurally highly similar. At the same time, there are clear differences between the Nordic countries regarding their national images. The purpose of this study is to a examine the relationship between ideas of the Nordic and national images through a qualitative study of brand manifestations on Nordic web portals for foreign visitors.Design/methodology/approachThe two guiding research questions are: How do Nordic branding strategies and national stereotypes impact on nation-branding content toward visitors in the Nordic region? What traces of the Nordic as a supranational concept can be found when the Nordic is translated into concrete national brand manifestations? The analysis focuses on brand manifestations such as brand visions, codes of expression, differentiation, narrative identity and ideologies.FindingsThe analysis shows that clichés about the nations prevail in contemporary brand material and that Nordic branding strategies impact on the portals in diffuse and implicit ways. There are, however, some important common denominators, pointing toward a new Nordic brand related to exotic, untouched yet easily accessible nature, with a focus on pure, fresh and clean food with new tastes, in combination with happy and welcoming people.Originality/valueThe results from the study contribute with insight in how ideas of the Nordic on a supranational level transform when used in concrete and practical branding material. Further, this paper proposes a new Nordic branding focus, which contests traditional Nordic ideas.
The gains and pains of small and medium-scale enterprises (SMEs): the way forward for entrepreneurship development in Nigeria
Authors: Olaore Gbemi Oladipo , Adejare Bimbo Onaolapo , Udofia Ekpenyong Ekpenyong 
Published: March 2021

Purpose
The purpose of this study is to assess the role of small and medium-scale enterprises (SMEs) as a catalyst to all things good in great economies; however, sadly, Nigeria has been unable to unlock SME development and the many benefits. The paper’s examination revolves around SMEs and entrepreneurial development, employment generation, government policies and financial aid and its availability. With the intention of establishing the relevance of government role in creating vibrant economies via thriving SMEs and its ripple effect on employment generation.

Design/methodology/approach
The study adopts a survey design, using a questionnaire for data gathering and percentile, confirmatory factor analysis (CFA) and structural equation modelling (SEM) for data analysis.

Findings
The study established a significant direct relationship between entrepreneurship development and infrastructure development and employment generation. Also, there was a significant direct relationship between government policies and infrastructure development. However, surprisingly, there was an insignificant relationship between government policy and financial aid and accessibility.

Practical implications
The government’s role in SMEs’ survival and entrepreneurship development is invaluable. The government must live up to their bidding and create an enabling environment to promote SME and entrepreneurship growth. Only this will transform the economy and minimize unemployment to its barest minimum.

Originality/value
The study’s research model is an interesting contribution to the body of work in SME and entrepreneurship development. The study is also an original attempt at having a good representation of the South-Western part of Nigeria, as research in high impact journals is usually domiciled in one state.
Modelling the comparative costs of Namaste Care: results from the namaste care intervention UK study
Authors: Bray Jennifer , Brooker Dawn , Latham Isabelle , Baines Darrin 
Published: March 2021

Purpose
The purpose of this paper is to populate a theoretical cost model with real-world data, calculating staffing, resource and consumable costs of delivering Namaste Care Intervention UK (NCI-UK) sessions versus “usual care” for care home residents with advanced dementia.

Design/methodology/approach
Data from five care homes delivering NCI-UK sessions populated the cost model to generate session- and resident-level costs. Comparator usual care costs were calculated based on expert opinion and observational data. Outcome data for residents assessed the impact of NCI-UK sessions and aligned with the resident-level costs of NCI-UK.

Findings
NCI-UK had a positive impact on residents’ physical, social and emotional well-being. An average NCI-UK group session cost £220.53, 22% more than usual care, and ran for 1.5–2 h per day for 4–9 residents. No additional staff were employed to deliver NCI-UK, but staff-resident ratios were higher during Namaste Care. Usual care costs were calculated for the same time period when no group activity was organised. The average cost per resident, per NCI-UK session was £38.01, £7.24 more than usual care. In reality, costs were offset by consumables and resources being available from stock within a home.

Originality/value
Activity costs are rarely calculated as the focus tends to be on impact and outcomes. This paper shows that, although not cost neutral as previously thought, NCI-UK is a low-cost way of improving the lives of people living with advanced dementia in care homes.
Coral degradation impairs learning of non‐predators by Whitetail damselfish
Authors: Chivers Douglas P. , McCormick Mark I. , Fakan Eric P. , Edmiston Jake W. , Ferrari Maud C. O. 
Published: March 2021

Abstract

A prerequisite for effective antipredator responses is the ability of a prey to distinguish animals that pose a threat from those that do not. Prey often have efficient learning mechanisms to learn threats but learning to recognize nonpredators may be equally or more important. Moreover, the ability to generalize learned information is of key importance for prey animals. Prey take information they know about one species to make ‘educated guesses’ about the predatory/nonpredatory status of other unknown species.

Here, we investigate the ability of Whitetail damselfish Pomacentrus chrysurus to learn the identity of non‐predators and then generalize their responses to other unknown animals. Our work is completed within the context of unprecedented habitat degradation in reef ecosystems. When corals die, the remaining skeleton is colonized by algae, cyanobacteria and sessile invertebrates. These opportunistic colonists change the physical and chemical landscape of the reef and hence the background odour in which predator and non‐predator recognition occurs.

Our results indicated that Whitetail damselfish learn to classify Moonwrasse Thalasomma lunare as a non‐predator through the process of latent inhibition, whereby the prey are repeatedly exposed to Moonwrasse odour multiple times in the absence of negative reinforcement. These fish subsequently generalized their nonpredator recognition to other unknown wrasse, but not distantly related fish. Of key importance was our finding that the patterns and extent of non‐predator learning and generalization were dramatically altered in dead coral habitats. As predicted, prey that learned the Moonwrasse as a nonpredator in live coral environments did not subsequently respond to Moonwrasse when we tried to teach them Moonwrasse was a predator in live coral. However, this non‐predator recognition was reduced in dead coral environments. Moreover, generalization completely failed when we changed from live to dead coral environments.

Juvenile damselfishes need to rapidly catalogue the identity of unknown animals when they arrive at a reef. Changing background odours, that occur with changing tides and currents, means that prey need to learn non‐predator identities separately in each water source. This cognitive challenge likely has significant survival consequence in a changing environment.

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