bluuebunny/crossref_metadata_2025_split huggingface dataset:
COVID-19 Epidemic in Switzerland: Growth Prediction and Containment Strategy Using Artificial Intelligence and Big Data
Authors: Marini Marcello , Chokani Ndaona , Abhari Reza S. 
Published: April 2020

AbstractUsing a previously developed agent-based artificial intelligence simulation platform (EnerPol) coupled with ‘Big Data,’ the evolution and containment of COVID-19 in Switzerland is examined. The EnerPol platform has been used in a broad range of case studies in different sectors in all of Europe, USA, Japan, South Korea and sub Saharan Africa over the last 10 years. In the present study, the entire Swiss population (8.57 million people), including cross-border commuters, and the entire Swiss public and private transport network that is simulated to assess transmission of the COVID-19 virus. The individual contacts within the population, and possible transmission pathways, are established from a simulation of daily activities that are calibrated with micro-census data. Various governmental interventions with regards to closures and social distancing are also implemented. The epidemiology of the COVID-19 virus is based on publicly available statistical data and adapted to Swiss demographics. The predictions estimate that between 22 February and 11 April 2020, there will be 720 deaths from 83’300 COVID-19 cases, and 73’300 will have recovered; our preliminary variability in these estimates is about 21% over the aforementioned period. In the absence of governmental intervention, 42.7% of the Swiss population would have been infected by 25 April 2020 compared to our prediction of a 1% infection over this time period, saving thousands of lives. It is argued that future scenarios regarding relaxation of the lockdown should be carefully simulated, as by 19 April 2020, there will still remain a substantial number of infected individuals, who could retrigger a second spread of COVID-19. Through the use of a digital tool, such as Enerpol, to evaluate in a data-driven manner the impacts of various policy scenarios, the most effective measures to mitigate a spread of COVID-19 can be devised while we await the deployment of large-scale vaccination for the population globally. By tailoring the spatio-temporal characteristics of the spread to match the capacity of local healthcare facilities, appropriate logistic needs can be determined, in order not to overwhelm the health care services across the country.
How will this continue? Modelling interactions between the COVID-19 pandemic and policy responses
Authors: Rossberg Axel G. , Knell Robert J. 
Published: April 2020

AbstractMuch of the uncertainty about the progression of the COVID-19 pandemic stems from questions about when and how non-pharmaceutical interventions (NPI) by governments, in particular social distancing measures, are implemented, to what extent the population complies with these measures, and how compliance changes through time. Further uncertainty comes from a lack of knowledge of the potential effects of removing interventions once the epidemic is declining. By combining an epidemiological model of COVID-19 for the United Kingdom with simple sub-models for these societal processes, this study aims to shed light on the conceivable trajectories that the pandemic might follow over the next 1.5 years. We show strong improvements in outcomes if governments review NPI more frequently whereas, in comparison, the stability of compliance has surprisingly small effects on cumulative mortality. Assuming that mortality does considerably increase once a country’s hospital capacity is breached, we show that the inherent randomness of societal processes can lead to a wide range of possible outcomes, both in terms of disease dynamics and mortality, even when the principles according to which policy and population operate are identical.. Our model is easily modified to take other aspects of the socio-pandemic interaction into account.
Exploring Ruthenium-based organometallic inhibitors against Plasmodium Calcium Dependent Kinase 2 (PfCDPK2): a combined ensemble docking, QM paramterization and molecular dynamics study
Authors: Patel Dhaval , Athar Mohd , Jha Prakash C. 
Published: April 2020

ABSTRACTRecent advances in the metal-organic framework (MOF) have accelerated the discovery of novel metal-based anticancer, antibacterial and antimalarial compounds. This is substantiated by many serendipitously discovered metals (Ru, Rh, and Ir) based inhibitors that established the importance of metal inserted into the known organic scaffold. Conversely, it is possible to design novel bioactive compounds by mimicking hypervalent carbon atoms by transition metals. This process can be facilitated by computational drug discovery by treating metal center using optimized parameters that can be used for molecular docking and molecular dynamics simulations. Further, the method can be plugged with high computational power and refined algorithms to interpret chemical phenomena with atomic-level insights. In the present work, we have demonstrated an approach for parameterizing three organometallic ligands (FLL, E52, and staurosporine) using MCPB.py. In particular, we report that E52 and FLL have a better shape complimentary and affinity compared to staurosporine identified inhibitor (staurosporine) against Calcium-dependent protein kinases 2 (CDPK2). This study also revealed that a flexible approach (ensemble) outperforms for the given target with dynamic movements. The calculated MMPBSA energies for staurosporine, FLL and E52 were −66.461 ± 2.192, −67.182 ± 1.971 and −91.339 ± 2.745 kcal/mol respectively.
Purifying selection can reduce intraspecific mitochondrial gene variation to that of nuclear rRNA
Authors: Matumba Tshifhiwa G. , Oliver Jody , Barker Nigel P. , McQuaid Christopher D. , Teske Peter R. 
Published: April 2020

AbstractMitochondrial DNA (mtDNA) has long been used to date the divergence between species, and to explore the time when species’ effective population sizes changed. The idea that mitochondrial DNA is useful for molecular dating rests on the premise that its evolution is neutral. This premise was questionable to begin with, and even though it has long been challenged, the evidence against clock-like evolution of mtDNA is usually ignored. Here, we present a particularly clear and simple example to illustrate the implications of violations of the assumption of selective neutrality. DNA sequences were generated for the mtDNA COI gene and the nuclear 28S rRNA of two closely related and widely distributed rocky shore snails whose geographical ranges are defined by different thermal preferences. To our knowledge, this is the first study to use nuclear rRNA sequence for studying species-level genealogies instead of phylogenetics, presumably because this marker is considered to be uninformative at this taxonomic level. Even though the COI gene evolves at least an order of magnitude faster, which was reflected in high inter-specific divergence, intraspecific genetic variation was similar for both markers. As a result, estimates of population expansion times based on mismatch distributions were completely different for the two markers. Assuming that 28S evolves effectively clock-like, these findings likely illustrate variation-reducing purifying selection in mtDNA at the species level, and an elevated divergence rate caused by divergent selection between the two species. Although these two selective forces together make mtDNA suitable as a DNA barcoding marker because they create a ‘barcoding gap’, estimates of demographic change can be expected to be highly unreliable. Our study contributes to the growing evidence that the utility of mtDNA beyond DNA barcoding is limited.
Changes amid constancy: flower and leaf microbiomes along land use gradients and between bioregions
Authors: Gaube Paul , Junker Robert R. , Keller Alexander 
Published: April 2020

AbstractMicrobial communities inhabiting above-ground parts of plants affect their host’s development, fitness and function. Although studies on plant-associated microbes are of growing interest, environmental drivers of flower microbiomes in particular are poorly characterized. In this study, we investigated flower and leaf epiphytic bacterial microbiomes ofRanunculus acrisandTrifolium pratenseusing metabarcoding of 16S ribosomal DNA in three German bioregions and along land-use intensity gradients. Our data suggests that the structures of bacterial communities clearly differed between plant species and tissue types. Also, floral bacterial communities ofR. acrisshowed higher variability in comparison toT. pratense. Bacteria usually associated with pollinators were found solely in flower samples, while such usually associated with the rhizosphere were only present in high abundances on leaves. We identified Pseudomonadaceae, Enterobacteriaceae and Sphingomonadaceae as the most abundant taxa on flowers, while Sphingomonadaceae, Methylobacteriaceae and Cytophagaceae dominated bacterial communities on leaves. We found strong bacterial turnover already for short geographic distances, which however did not increase with the long distances between bioregions. High land use intensity caused phylogenetically less diverse and more homogenous bacterial communities. This was associated with a loss of rare bacterial families. Intensification of mowing and fertilization affected almost all plant associated bacterial communities, while grazing had only minor effects on bacterial structures ofT. pratenseflowers. However, dominant taxa were mostly resilient to mowing, grazing and fertilization. Despite that, we identified indicator taxa for regularly disturbed environments in flower microbiomes.
Comparative study of contact repulsion in control and mutant macrophages using a novel interaction detection
Authors: Solís-Lemus JA , Sánchez-Sánchez BJ , Marcotti S , Burki M , Stramer B , Reyes-Aldasoro CC 
Published: April 2020

AbstractThis paper compares the contact-repulsion movement of mutant and wild-type macrophages using a novel interaction detection mechanism. The migrating macrophages are observed inDrosophilaembryos. The study is carried out by a framework calledmacrosight, which analyses the movement and interaction of migrating macrophages. The framework incorporates a segmentation and tracking algorithm into analysing motion characteristics of cells after contact. In this particular study, the interactions between cells is characterised in the case of control embryos and Shot3mutants, where the cells have been altered to suppress a specific protein, looking to understand what drives the movement. Statistical significance between control and mutant cells was found when comparing the direction of motion after contact in specific conditions. Such discoveries provide insights for future developments in combining biological experiments to computational analysis. Cell Segmentation, Cell Tracking, Macrophages, Cell Shape, Contact Analysis
ULTRASOUND-ASSISTED MAGNETIC NANOPARTICLE-BASED GENE DELIVERY
Authors: Zhang Wei , Abdelrasoul Gaser N. , Savchenko Oleksandra , Abdrabou Abdalla , Wang Zhixiang , Chen Jie 
Published: April 2020

AbstractLow-intensity pulsed ultrasound (LIPUS), a special type of ultrasonic stimulation, is attracting a lot of attention for both clinical and scientific research. In this paper, we report a concept of a new method using magnetic nanoparticles (MNPs) for LIPUS-assisted gene delivery. The MNPs are iron oxide superparamagnetic nanoparticles, coated with polyethyleneimine (PEI), which introduces a high positive surface charge, favorable for the binding of genetic material. Due to the paramagnetic properties of the MNPs, the application of an external magnetic field increases transfection efficiency; meanwhile, LIPUS stimulation enhances cell permeability. We found out that stimulation at the intensity of 30 mW/cm2for 10 minutes yields optimal results with a minimal adverse effect on the cells. Combining the effect of the external magnetic field and LIPUS, the genetic material (GFP or Cherry Red plasmid in our case) can enter the cells. The flow cytometry results showed that by using just a magnetic field to direct the genetic material, the transfection efficiency of HEK 293 cells that were treated with our MNPs was 56.1%. Coupled with LIPUS stimulation, it increased to 61.5% or 19% higher than the positive control (Lipofectamine 2000). In addition, compared with the positive control, our method showed less toxicity. Cell viability after transfection was 63.61%, 19% higher than with the standard transfection technique. In conclusion, we designed a new gene-delivery technique that is affordable, targeted, shows low-toxicity, yet high transfection efficiency, compared to other conventional approaches.The Graphical Abstract
Hidden biodiversity in Neotropical streams: DNA barcoding uncovers high endemicity of freshwater macroinvertebrates at small spatial scales
Authors: De León Luis F. , Cornejo Aydeé , Gavilán Ronnie G. , Aguilar Celestino 
Published: April 2020

AbstractAquatic macroinvertebrates play a crucial role in freshwater ecosystems, but their diversity remains poorly known, particularly in the tropics. This “taxonomic void” represents limits our understanding of biodiversity patterns and processes in freshwater ecosystems, and the scale at which they operate. We used DNA barcoding to estimate lineage diversity (and the diversity of unique haplotypes) in 224 specimens of freshwater macroinvertebrates at a small spatial scale within the Panama Canal Watershed (PCW). In addition, we compiled available barcoding data to assess macroinvertebrate diversity at a broader spatial scale spanning the Isthmus of Panama. Consistently across two species delimitation algorithms (i.e., ABGD and GMYC), we found high lineage diversity within the PCW, with ~ 100-106 molecular operational taxonomic units (MOTUs at 2% sequence divergence) across 168 unique haplotypes. We also found a high lineage diversity along the Isthmus of Panama, but this diversity peaked within the PCW. However, our rarefaction/extrapolation approach showed that this diversity remains under sampled. As expected, these results indicate that the diversity of Neotropical freshwater macroinvertebrates is higher than previously thought, with the possibility of high endemicity even at narrow spatial scales. Geographic isolation is likely a main factor shaping these patterns of diversity. However, local disturbances such as the rupture of the continental divide due to the construction of the Panama Canal might be reshaping these patterns of diversity at a local scale. Although further work is needed to better understand the processes driving diversification in freshwater macroinvertebrates, we suggest that Neotropical streams represent continental islands of diversity. Understanding these islands of diversity is crucial in the face of increasing human disturbance.
Borrelia afzeliidoes not suppress the development of anti-tick immunity in bank voles
Authors: Gomez-Chamorro Andrea , Li Yating , Herrera Adrian , Rais Olivier , Dautel Hans , Voordouw Maarten J. 
Published: April 2020

AbstractVector-borne pathogens manipulate their vertebrate hosts to enhance their transmission to arthropod vectors. The ability of vertebrate hosts to develop acquired immunity against arthropod vectors represents an existential threat for both the vector and the pathogen. The purpose of the study was to test whether the tick-borne spirochete bacteriumBorrelia afzeliicould suppress the development of acquired immunity to its tick vectorIxodes ricinusin the bank voleMyodes glareolus, which is an important host for both the tick and the pathogen. We created a group ofB. afzelii-infected bank voles and an uninfected control group by exposing lab-reared animals to infected or uninfected ticks. At 1, 2, and 3 months post-infection, all bank voles were infested with larvalI. ricinusticks. The bank voles developed a strong antibody response against tick salivary gland extract proteins. This anti-tick immunity had negative effects on tick fitness traits including engorged larval weight, unfed nymphal weight, larva-to-nymph molting time and larva-to-nymph molting success. Infection withB. afzeliidid not suppress the development of acquired immunity againstI. ricinusticks. The development of anti-tick immunity was strongly correlated with a dramatic temporal decline in both the bacterial abundance in the host ear tissues and the host-tick transmission success ofB. afzelii. Our study suggests that the development of anti-tick immunity in bank voles has important consequences for the density of infected ticks and the risk of Lyme borreliosis.ImportanceMany pathogens enhance their persistence and transmission by suppressing the immune system of their host. We used an experimental infection approach to test whether the Lyme disease pathogen,Borrelia afzelii, could suppress the development of acquired immunity against its tick vector (Ixodes ricinus) in the bank vole (Myodes glareolus), but found no evidence for this phenomenon. Uninfected andB. afzelii-infected bank voles both developed a strong IgG antibody response against tick salivary gland extract following repeated infestations withI. ricinusticks. The development of anti-tick immunity was negatively correlated with the abundance ofB. afzeliiin ear tissue biopsies and with host-to-tick transmission toI. ricinusticks. Our study suggests that anti-tick immunity in the bank vole reduces the prevalence of this important tick-borne pathogen.
A combined RNA-Seq and comparative genomics approach identifies 1,085 candidate structured RNAs expressed in human microbiomes
Authors: Fremin Brayon J. , Bhatt Ami S. 
Published: April 2020

AbstractStructured RNAs play varied bioregulatory roles within microbes. To date, hundreds of candidate structured RNAs have been predicted using informatic approaches by searching for motif structures in genomic sequence data. However, only a subset of these candidate structured RNAs, those from culturable, well-studied microbes, have been shown to be transcribed. As the human microbiome contains thousands of species and strains of microbes, we sought to apply both informatic and experimental approaches to these organisms to identify novel transcribed structured RNAs. We combine an experimental approach, RNA-Seq, with an informatic approach, comparative genomics across the human microbiome project, to discover 1,085 candidate, conserved structured RNAs that are actively transcribed in human fecal microbiomes. These predictions include novel tracrRNAs that associate withCas9and RNA structures encoded in overlapping regions of the genome that are in opposing orientations. In summary, this combined experimental and computational approach enables the discovery of thousands of novel candidate structured RNAs.
Contemporary Enterovirus D68 strains show enhanced replication and translation at 37°C
Authors: Smith Brendan D. , Pekosz Andrew 
Published: April 2020

ABSTRACTEnterovirus D68 (EV-D68) emerged in 2014 as an important pathogen linked to severe lower respiratory disease and acute flaccid myelitis outbreaks. Historically associated with mild common-cold-like symptoms, clusters of severe disease attributed to EV-D68 appeared during a series of outbreaks in 2014, 2016, and 2018. Previous studies of historic EV-D68 strains demonstrated attenuated replication at temperatures of the lower respiratory tract (37°C), when compared to the upper respiratory tract (32°C). By testing a panel of historic and contemporary EV-D68 strains at 32°C and 37°C, we demonstrate that contemporary strains of EV-D68 undergo little to no attenuation at increased temperatures. Contemporary strains produced higher levels of viral proteins at 32°C and 37°C than historic strains, although both strains infected similar numbers of cells and had comparable amounts of replication complexes. IRES activity assays with dual-luciferase reporter plasmids demonstrated enhanced translation in recent EV-D68 strains mapped to regions of variability in the 5’ UTR found only in contemporary strains. Using an infectious clone system, we demonstrate that the translation advantage dictated by the 5’ UTR does not solely mediate temperature sensitivity. The strain-dependent effects of temperature on the EV-D68 life cycle gives insight into the susceptibility of the lower respiratory system to contemporary strains.IMPORTANCEEnterovirus-D68 (EV-D68) emerged in 2014 as a causative agent of biannual severe pediatric respiratory disease and acute flaccid myelitis (AFM). We show that recent EV-D68 viruses have gained the ability to replicate at 37°C. Enhanced virus protein translation seemed to correlate with enhanced virus replication at 37°C but other genetic factors are also contributing to this phenotype. An enhanced ability to replicate at core body temperature may have allowed EV-D68 to penetrate both lower in the respiratory tract and into the central nervous system, explaining the recent surge in severe disease associated with virus infection.
Kauai: Extending a fast-food brand into traditional retail as a growth strategy
Authors: de Reuck Shelley , Bick Geoff 
Published: April 2020

Subject area of the teaching case
The case can be used in the subject areas of marketing, strategy, business model innovation in an emerging market. The case introduces a practical example of brand extension as a growth strategy employed by an existing brand to secure additional revenue channels and customer touch points.

Student level
This teaching case is aimed at postgraduate business students such as Master's degrees in Business Administration degrees, postgraduate diplomas, executive education, or specialist Master's degrees.

Brief overview of the teaching case
Kauai is a health restaurant with 150 stores across South Africa, Namibia and Botswana, more than 50% of which are franchise-owned. An acquisition of the original Kauai quick-service restaurant (QSR) chain by Real Foods in 2015 leads to a complete rebrand and overhaul of its product offering and store experience. Since the acquisition, the business operates as a startup with few formal processes and KPIs in place to drive performance. Despite the obvious success the team is battling with the factors that need to be considered to ensure that they can scale adequately to realise full potential. Plus how should they position the existing brand effectively within the FMCG space to maximise the contribution of brand equity to its success?

Expected learning outcomes

–The understanding around the business model of a strong, existing brand entering a highly competitive and price-sensitive FMCG.
–Analysing the marketing strategy and brand identity approaches that could be used.
–An understanding of the brand extension strategy that could be implemented in light of various challenges.
–Understanding how retail marketing works in an emerging market context.