bluuebunny/crossref_metadata_2025_split huggingface dataset:
Physiological roles of short-chain and long-chain menaquinones (vitamin K2) in Lactococcus cremoris
Authors: Liu Yue , Charamis Nikolaos , Boeren Sjef , Blok Joost , Lewis Alisha Geraldine , Smid Eddy J. , Abee Tjakko 
Published: November 2021

AbstractLactococcus cremoris and L. lactis are well-known for their occurrence and applications in dairy fermentations, but their niche extends to a range of natural and food production environments. L. cremoris and L. lactis produce MKs (vitamin K2), mainly as the long-chain forms represented by MK-9 and MK-8, and a detectable amount of short-chain forms represented by MK-3. The physiological significance of the different MK forms in the lifestyle of these bacterial species has not been investigated extensively. In this study, we used L. cremoris MG1363 to construct mutants producing different MK profiles by deletion of genes encoding (i) a menaquinone-specific isochorismate synthase, (ii) a geranyltranstransferase and (iii) a prenyl diphosphate synthase. These gene deletions resulted in (i) a non-MK producer (ΔmenF), (ii) a presumed MK-1 producer (ΔispA) and (iii) a MK-3 producer (Δllmg_0196), respectively. By examining the phenotypes of the MG1363 wildtype strain and respective mutants, including biomass accumulation, stationary phase survival, oxygen consumption, primary metabolites, azo dye/copper reduction, and proteomes, under aerobic, anaerobic and respiration-permissive conditions, we could infer that short-chain MKs like MK-1 and MK-3 are preferred to mediate extracellular electron transfer and reaction with extracellular oxygen, while the long-chain MKs like MK-9 and MK-8 are more efficient in aerobic respiratory electron transport chain. The different electron transfer routes mediated by short-chain and long-chain MKs likely support growth and survival of L. cremoris in a range of (transiently) anaerobic and aerobic niches including food fermentations, highlighting the physiological significance of diverse MKs in L. cremoris.
Estimating the transmissibility of SARS-CoV-2 during periods of high, low and zero case incidence
Authors: Golding Nick , Price David J. , Ryan Gerard E. , McVernon Jodie , McCaw James M. , Shearer Freya M. 
Published: November 2021

AbstractAgainst a backdrop of widespread global transmission, a number of countries have successfully brought large outbreaks of COVID-19 under control and maintained near-elimination status. A key element of epidemic response is the tracking of disease transmissibility in near real-time. During major outbreaks, the reproduction rate can be estimated from a time-series of case, hospitalisation or death counts. In low or zero incidence settings, knowing the potential for the virus to spread is a response priority. Absence of case data means that this potential cannot be estimated directly.We present a semi-mechanistic modelling framework that draws on time-series of both behavioural data and case data (when disease activity is present) to estimate the transmissibility of SARS-CoV-2 from periods of high to low – or zero – case incidence, with a coherent transition in interpretation across the changing epidemiological situations. Of note, during periods of epidemic activity, our analysis recovers the effective reproduction number, while during periods of low – or zero – case incidence, it provides an estimate of transmission risk. This enables tracking and planning of progress towards the control of large outbreaks, maintenance of virus suppression, and monitoring the risk posed by re-introduction of the virus.We demonstrate the value of our methods by reporting on their use throughout 2020 in Australia, where they have become a central component of the national COVID-19 response.
Roflumilast, a Phosphodiesterase-4 Inhibitor, Ameliorates Sleep Deprivation-Induced Cognitive Dysfunction in C57BL/6J Mice
Authors: Bhat Abid , Bishir Muhammed , Pandi-Perumal Seithikurippu R. , Chang Sulie , Chidambaram Saravana B. 
Published: November 2021

ABSTRACTSleep deprivation (SD) interferes with long-term memory and cognitive functions by over-activation of phosphodiesterase (PDEs) enzymes. PDE4, a non-redundant regulator of the cyclic nucleotides (cAMP), is densely expressed in the hippocampus and is involved in learning and memory processes. In the present study, we investigated the effects of Roflumilast (ROF), a PDE4B inhibitor, on sleep deprivation induced cognitive dysfunction in a mouse model. Memory assessment was performed using a novel object recognition task and the hippocampal cAMP level was estimated by the ELISA method. The alterations in the expressions of PDE4B, amyloid-beta (Aβ), CREB, BDNF, and synaptic proteins (Synapsin I, SAP 97, PSD 95) were assessed to gain insights into the possible mechanisms of action of ROF using the Western blot technique. Results show that ROF reversed SD induced cognitive decline in mice. ROF down-regulated PDE4B and Aβ expressions in the brain. Additionally, ROF improved the cAMP level and the protein expressions of synapsin I, SAP 97, and PSD 95 in the hippocampal region of SD mice. Taken together, these results suggest that ROF can suppress the deleterious effects of SD-induced cognitive dysfunction via the PDE4B-mediated cAMP/CREB/BDNF signaling cascade.
Metabolic analysis of a bacterial synthetic community from maize roots provides new mechanistic insights into microbiome stability
Authors: Krumbach Jenna , Kroll Patrizia , Wewer Vera , Metzger Sabine , Ischebeck Till , Jacoby Richard P. 
Published: November 2021

AbstractStability is a desirable property for agricultural microbiomes, but there is a poor understanding of the mechanisms that mediate microbial community stability. Recently, a representative bacterial synthetic community from maize roots has been proposed as a model system to study microbiome stability (Niu 2017, PNAS, 114:E2450). This SynCom assembles stably when all seven members are present, but community diversity collapses without the keystone E. cloacae strain. The aim of this study was to assess the role of metabolites for the stability of this SynCom, by defining the metabolic niches occupied by each strain, as well as their cross-feeding phenotypes and B-vitamin dependencies. We show that the individual member strains occupy complementary metabolic niches, measured by the depletion of distinct metabolites in exometabolomic experiments, as well as contrasting growth phenotypes on diverse carbon substrates. Minimal medium experiments show that the established seven-member community comprises a mixture of prototrophic and auxotrophic strains. Correspondingly, experimental cross-feeding phenotypes showed that spent media harvested from the prototrophic strains can sustain growth of two auxotrophs. We suggest that the metabolic mechanisms exhibited by this SynCom could serve as design principles to inform the rational assembly of stable plant-associated microbial communities.
Targeted profiling of human extrachromosomal DNA by CRISPR-CATCH
Authors: Hung King L. , Luebeck Jens , Dehkordi Siavash R. , Coruh Ceyda , Law Julie A. , Greenleaf William J. , Mischel Paul , Bafna Vineet , Chang Howard Y. 
Published: November 2021

ABSTRACTExtrachromosomal DNA (ecDNA) is a common mode of oncogene amplification but is challenging to analyze. Here, we present a method for targeted purification of megabase-sized ecDNA by combining in-vitro CRISPR-Cas9 treatment and pulsed field gel electrophoresis of agarose-entrapped genomic DNA (CRISPR-CATCH). We demonstrate strong enrichment of ecDNA molecules containing EGFR, FGFR2 and MYC from human cancer cells. Targeted purification of ecDNA versus chromosomal DNA enabled phasing of genetic variants and provided definitive proof of an EGFRvIII mutation on ecDNA and wild-type EGFR on chromosomal DNA in a glioblastoma neurosphere model. CRISPR-CATCH followed by nanopore sequencing enabled single-molecule ecDNA methylation profiling and revealed hypomethylation of the EGFR promoter on ecDNA compared to the native chromosomal locus in the same cells. Finally, separation of ecDNA species by size and sequencing allowed accurate reconstruction of megabase- sized ecDNA structures with base-pair resolution. CRISPR-CATCH is a new addition to the toolkit for studying focal amplifications in cancer and will accelerate studies aiming to explore the genetic and epigenetic landscapes of ecDNA.
Diagnostic performance of attenuated total reflection Fourier-transform infrared spectroscopy for detecting COVID-19 from routine nasopharyngeal swab samples
Authors: Heino Helinä , Rieppo Lassi , Männistö Tuija , Sillanpää Mikko J. , Mäntynen Vesa , Saarakkala Simo 
Published: November 2021

AbstractSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causing global COVID-19 pandemic since 2019 has led to increasing amount of research to study how to do fast screening and diagnosis to efficiently detect COVID-19 positive cases, and how to prevent spreading of the virus. Our research objective was to study whether SARS-CoV-2 could be detected from routine nasopharyngeal swab samples by using attenuated total reflection Fourier-transform infrared (ATR-FTIR) spectroscopy coupled with partial least squares discriminant analysis (PLS-DA). The advantage of ATR-FTIR is that measurements can be conducted without any sample preparation and no reagents are needed. Our study included 558 positive and 558 negative samples collected from Northern Finland. Overall, we found moderate diagnostic performance for ATR-FTIR when polymerase chain reaction (PCR) was used as the gold standard: the average area under the receiver operating characteristics curve (AUROC) was 0.67-0.68 (min. 0.65, max. 0.69) with 20, 10 and 5 k-fold cross validations. Mean accuracy, sensitivity and specificity was 0.62-0.63 (min. 0.60, max. 0.65), 0.61 (min. 0.58, max. 0.65) and 0.64 (min. 0.59, max. 0.67) with 20, 10 and 5 k-fold cross validations. As a conclusion, our study with relatively large sample set clearly indicate that measured ATR-FTIR spectrum contains specific information for SARS-CoV-2 infection (P<0.001 in label permutation test). However, the diagnostic performance of ATR-FTIR remained only moderate, potentially due to low concentration of viral particles in the transport medium. Further studies are needed before ATR-FTIR can be recommended for fast screening of SARS-CoV-2 from routine nasopharyngeal swab samples.ImportanceAttenuated total reflection Fourier-transform infrared (ATR-FTIR) spectroscopy coupled with machine learning-based analysis was applied to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from nasopharyngeal swab samples originally collected and processed for polymerase chain reaction (PCR) analysis. Even though our results showed moderate performance, we think that our carefully designed and conducted work is valuable in the field of SARS-CoV-2 diagnostics as there were as many as 1116 nasopharyngeal swab samples (558 negative and 558 positive) collected from individual patients in a real clinical setting. The Real clinical setting refers to the fact that the nasopharyngeal swab samples were collected from people with symptoms typical for COVID-19 or asymptomatic individuals exposed to SARS-CoV-2. The presented technique could be relatively easy to use for point-of-care testing, as ATR-FTIR can be performed with a portable machine without sample preparation and machine learning-based model could give a result immediately after ATR-FTIR measurement.
Structural basis of INTAC-regulated transcription
Authors: Zheng Hai , Jin Qianwei , Qi Yilun , Liu Weida , Ren Yulei , Wang Xinxin , Chen Fei , Cheng Jingdong , Chen Xizi , Xu Yanhui 
Published: November 2021

AbstractFor the majority of expressed eukaryotic genes, RNA polymerase II (Pol II) forms a paused elongation complex (PEC) and undergoes promoter-proximal pausing downstream of the transcription start site 1–3. The polymerase either proceeds into productive elongation or undergoes promoter-proximal premature transcription termination 4–6. It remains incompletely understood how transcription is regulated at this stage. Here, we determined the structure of PEC bound to INTAC, an Integrator-containing PP2A complex 7, at near-atomic resolution. The structure shows that INTAC partially wraps around PEC through multiple contacts, permitting the memetic nascent RNA to run into substrate-entry tunnel of the endonuclease subunit INTS11 of INTAC for cleavage. Pol II C-terminal domain (CTD) winds over INTAC backbone module through multiple anchors and is suspended above the phosphatase of INTAC for dephosphorylation. Biochemical analysis shows that INTAC-PEC association requires unphosphorylated CTD and could tolerate CTD phosphorylation, suggesting an INTAC-mediated persistent CTD dephosphorylation followed by reinforcement of the INTAC-PEC complex. Our study reveals how INTAC binds PEC and orchestrates RNA cleavage and CTD dephosphorylation, two critical events in generating premature transcription termination.
The evolution of neurosensation drives the gain and loss of phenotypic plasticity
Authors: Chen Emily Y. , Adams Diane K. 
Published: November 2021

AbstractPhenotypic plasticity is widely regarded as important for enabling species resilience to environmental change and for species evolution. However, insight into the complex mechanisms by which phenotypic plasticity evolves in nature has been limited by our ability to reconstruct evolutionary histories of plasticity. By using part of the molecular mechanism, we were able to trace the evolution of pre-feeding phenotypic plasticity across the class Echinoidea and identify the origin of plasticity at the base of the regular urchins. The neurosensory foundation for plasticity was ancestral within the echinoids. However, coincident development of the plastic trait and the neurosensory system was not achieved until the regular urchins, likely due to pleiotropic effects and linkages between the two colocalized systems. Plasticity continues to evolve within the urchins with numerous instances of losses associated with loss of sensory capabilities and in one case loss of neurons, consistent with a cost associated with maintaining these capabilities. Thus, evidence was found for the neurosensory system providing opportunities and constraints to the evolution of phenotypic plasticity.
Basic Health Units services quality assessment through Kano and SERVQUAL models
Authors: Lacerda Anderson Barbosa , Souza Augusto Sérgio da Silva , Da Silva Glycia Keylla Lucia , Azevedo Eduardo H. Malheiros De , Melo Fagner José Coutinho De 
Published: November 2021

PurposeThe present research aims to evaluate the quality of services provided by the Basic Health Units (UBS) of the Unified Health System (SUS) located in the city of Recife, in the state of Pernambuco, Brazil, using the Kano model integrated with the dimensions of quality proposed by the service quality (SERVQUAL) model.Design/methodology/approachThe research was classified as bibliographic, descriptive, quantitative and surveyable. A structured questionnaire based on the Kano Model integrated with the dimensions of quality proposed by the SERVQUAL model, applied online through Google Forms. The questionnaires were distributed on social networks, obtaining a non-probabilistic sample of 120 individuals, collected for convenience.FindingsThrough the analysis of the Kano Model, it was possible to observe that all the investigated attributes are classified as one-dimensional. Among the attributes that deserve to be highlighted are attributes “Clean and pleasant environment”, “Reliability and security of information”, “Knowledge of employees to perform services”, “Service performed in the promised time”, “Polite and kind staff in dealing with users” and “Effectiveness of the service provided” due to having the longest intervals when considering the satisfaction and dissatisfaction coefficients, above 1.575. These attributes must be considered as critical priorities when implementing improvements, since their presence considerably increases users' satisfaction, as well as their absence generates great dissatisfaction.Originality/valueThe research is original and justified by the potential use of a quality assessment tool in the public health service, especially primary care. It is noteworthy that there are few works that integrate the Kano and SERVQUAL models applied in the public health service and that this integration can contribute to the national and international literature, mainly in the identification and prioritization of areas for improvement.
Developing and testing a framework for understanding refugees' job search processes
Authors: Boss Harrison C.D. , Lee Clara S. , Bourdage Joshua S. , Hamilton Leah K. 
Published: November 2021

PurposeThis article outlines the development of the Refugee Job Search Process Framework (RJSPF), which was created to help identify barriers that refugees face when trying to find employment. The framework incorporates an interdisciplinary, multi-level approach to the job search, delving into research from migration studies and Industrial/Organizational psychology to outline factors that exist on both the side of the refugee applicant and the organization at each stage of the RJSPF. The authors also tested the RJSPF with Syrian refugees and service providers in Canada to examine the validity of each component of the model.Design/methodology/approachThe authors used a semi-structured format to interview refugees and service providers on their experiences in either trying to find employment or helping their refugee clients with the job search process. After transcribing the interviews, the data were independently coded, quantified, and analysed using Nvivo software to validate the RJSPF.FindingsThe majority of the RJSPF either had high or moderate support from the interviews. The authors also identified 6 broader themes using thematic analysis, which include language fluency, credential recognition, Canadian experience “catch 22”, cultural incongruencies, employer exploitation, and mental health for successful employment.Originality/valueThe RJSPF is a new integration of disparate theories of job search experiences in a literature that lacks an organizing framework and perspective on the unique challenges refugees face in this area compared to other newcomers. In doing so, the authors use an interdisciplinary, multi-level approach that extends the nomological network of barriers facing refugees, therefore informing future research and practice.
Exploring the impact of positing entrepreneurship in nature of science: initial science teachers' perspectives
Authors: Kaya-Capocci Sila , McCormack Orla , Erduran Sibel , Birdthistle Naomi 
Published: November 2021

PurposeThe social aspects of nature of science (NOS) have become more eminent but entrepreneurial perspectives of NOS continue to be neglected. Entrepreneurship is relevant to NOS and science education due to its role in scientific enterprises and its importance as a 21st-century skill required in all subjects, particularly in science, technology, engineering and math (STEM) subjects. Due to the impact of initial teacher education (ITE) and the science curriculum on Initial Science Teachers' (ISTs) understanding, the paper aims to explore the impact of including entrepreneurship in NOS with ISTs.Design/methodology/approachThe qualitative study investigated the changes in three ISTs by examining their understanding of entrepreneurship within NOS and their perspectives on the inclusion of entrepreneurship in the science curriculum following an intervention. The results were analysed through thematic and network analysis (NA).FindingsThe results indicated that following an intervention, ISTs developed a more holistic understanding of entrepreneurship in NOS and could see the benefits and rationale for including entrepreneurship in the science curriculum. However, certain concerns remained.Originality/valueAlthough entrepreneurship may contribute to NOS by promoting scientific development, enhancing interest in science and developing a holistic understanding of science, a thorough review of the relevant research literature suggests that studies investigating entrepreneurship in NOS are rare. The current paper fills this gap by exploring Irish ISTs' perspectives on positing entrepreneurship in NOS. The study suggests conducting further research on the integration of entrepreneurship in the science curriculum and its impact on ITE.
Antecedents and consequence of the consumer's psychic distance in cross-border e-commerce
Authors: Chen Xi , Kim Hag-Min 
Published: November 2021

PurposeThe psychic distance often hinders the interaction between cross-border e-commerce (CBEC) and consumers. This paper aims to discuss the issues of psychic distance of consumers in the CBEC. In addition, it attempts to explain the factors that affect psychic distance from three dimensions of culture, economy and politics and the two different shopping behaviors caused by psychic distance.Design/methodology/approachThis research incorporates both theoretical and empirical studies. In this study, 249 validated questionnaires were selected from 300 Chinese CBEC consumers by snowball sampling, and the relationship between variables was tested using structural equation model (SEM). This was done through online research, and it is ensured that the data obtained are first-hand information.FindingsThe paper suggests the theoretical model operationalizing CBEC psychic distance and the empirical analysis results show that all the six influencing factors have a positive impact on the psychic distance of consumers. Logistics infrastructure barriers in the economic dimension are confirmed as the major influencing factor, and the significance of the political dimension is relatively small. Based on consumers' uncertainty of various kinds of information, psychic distance subconsciously causes consumers to deviate in the cross-shopping process.Originality/valueCurrently, research on e-commerce mainly focuses on saving trade costs and improving consumer welfare, while research on the internal impact of CBEC on consumers is insufficient. Psychic distance is a new concept in the field of cultural and social research. The originality of this paper is that the concept of psychic distance has been extended from overseas invested enterprises to research with CBEC consumers as the selected object. The obstacles of CBEC have been widely studied, but few are related to the closeness of consumers, or the inner feelings of consumers are ignored. In the context of CBEC, this paper lists the actual external factors and potential threats that may affect consumers' consumption concerns of CBEC from three dimensions. The real emotions of consumers in the face of these difficulties indirectly affect the purchase satisfaction and reduce the purchase desire. Consumer psychic distance is a real phenomenon in cross-border shopping, and it is almost inevitable for these difficulties. On the premise of inevitability, high psychic distance will slow down cross-border shopping in the eyes of consumers.