bluuebunny/crossref_metadata_2025_split huggingface dataset:
The timing of contact restrictions and pro-active testing balances the socio-economic impact of a lockdown with the control of infections
Authors: Bej Saptarshi , Wolkenhauer Olaf 
Published: May 2020

AbstractDuring the SARS-CoV-2 pandemic, numerous mathematical models have been developed. Reporting artefacts and missing data about asymptomatic spreaders, imply considerable margins of uncertainty for model-based predictions. Epidemiological models can however also be used to investigate the consequences of measures to control the pandemic, reflected in changes to parameter values.We present a SIR-based, SUIR model in which the influence of testing and a reduction of contacts is studied by distinguishing ‘Unidentified’ and ‘Identified’ spreaders of infections. The model uses four ordinary differential equations and is kept deliberately simple to investigate general patterns occurring from testing and contact restrictions. The model goes beyond other efforts, by introducing time dependent parameter curves that represent different strategies in controlling the pandemic.Our analysis reveals the effect of ‘pro-active’ testing for the design of contact restriction measures. By pro-active testing we mean testing beyond those people who show symptoms. The simulations can explain why the timing of contract restrictions and pro-active testing is important. The model can also be used to study the consequence of different strategies to exit from lockdown.Our SUIR model is implemented in Python and is made available through a Juypter Notebooks. This an extensive documentation of the derivation and implementation of the model, as well as transparent and reproducible simulation studies. Our model should contribute to a better understanding of the role of testing and contact restrictions.
Effect of preventive actions and health care factors in controlling the outbreaks of COVID-19 pandemic
Authors: Abdulla Faruq , Nain Zulkar , Karimuzzaman Md. , Hossain Md. Moyazzem , Adhikari Utpal Kumar , Rahman Azizur 
Published: May 2020

AbstractWith the insurgence of the COVID-19 pandemic, a large number of people died in the past several months, and the situation is ongoing with increasing health, social and economic panic and vulnerability. Due to the lack of drugs and prophylaxis against COVID-19, most of the countries are now relying on maintaining social distance as preventative actions. However, this social distancing can create global socio-economic crisis and psychological disorders. Therefore, these control measures need to have an assessment to evaluate their value in containing the situation. In this study, we analyzed the outcome of COVID-19 in response to different control measures, health care facilities, and prevalent diseases. Based on our findings, the number of COVID-19 deaths found to be reduced with increased medical personnel and hospital beds. We found 0.23, 0.16, and 0.21 as the measurement of significant non-linear relationship between COVID-19 case fatality and number of physicians (p-value ≤ 7.1×10−6), nurses and midwives (p-value ≤ 4.6×10−3), and hospital beds (p-value ≤ 1.9×10−2). Importantly, we observed a significant correlation between the reduction of COVID-19 cases and the earliness of preventive initiation. As a result, enhancing health care facilities as well as imposing the control measures in a short time could be valuable to prevent the currently raging COVID-19 pandemic. The apathy of taking nation-wide immediate precaution measure has identified as one of the critical reasons to make the circumstances worst. Notably, countries including Gambia, Nicaragua, Burundi, Namibia, and Nepal have marked in a state of danger. Interestingly, no association between the comorbidities and severity of COVID-19 was found except for few diseases including cancer, which warranted further investigation at the pathobiological level. We believe that this study could be useful in developing a control strategy in COVID-19 as well as future pandemics.
Higher Temperature, Pressure, and Ultraviolet Are Associated with Less COVID-19 Prevalence – Meta-Regression of Japanese Prefectural Data
Authors: Takagi Hisato , Kuno Toshiki , Yokoyama Yujiro , Ueyama Hiroki , Matsushiro Takuya , Hari Yosuke , Ando Tomo 
Published: May 2020

AbstractA recent study from China suggests that high temperature and ultraviolet (UV) radiation cannot decrease the epidemics of Coronavirus disease 2019 (COVID-19). To determine whether COVID-19 prevalence is modulated by meteorological conditions, meta-regression of Japanese prefectural data was herein conducted. We extracted integrated number of patients testing positive for COVID-19 in each Japanese prefecture on 18 May 2020, population per 1-km2 inhabitable area in the prefecture in 2020, and monthly meteorological conditions at each prefectural capital city for 4 months (from January to April 2020). We averaged or cumulated the monthly data for the 4 months. To adjust for prefectural population density, we defined the COVID-19 prevalence as the integrated number of patients testing positive divided by the population per 100-km2 inhabitable area. Random-effects meta-regression was performed. A slope of the meta-regression line was significantly negative for mean air temperature (coefficient, −0.134; P = 0.019), mean sea level air pressure (−0.351; P = 0.001), and mean daily maximum UV index (−0.908; P = 0.012), which indicated that COVID-19 prevalence decreased significantly as air temperature, air pressure, and UV index increased. In conclusion, higher temperature, pressure, and UV may be associated with less COVID-19 prevalence, which should be confirmed by further epidemiological investigations taking other risk and protective factors of COVID-19 into account.
Local computational methods to improve the interpretability and analysis of cryo-EM maps
Authors: Kaur S. , Gomez-Blanco J. , Khalifa A. , Adinarayanan S. , Sanchez-Garcia R. , Wrapp D. , McLellan J. S. , Bui K. H. , Vargas J. 
Published: May 2020

AbstractCryo-electron microscopy (cryo-EM) maps usually show heterogeneous distributions of B-factors and electron density occupancies and are typically B-factor sharpened to improve their contrast and interpretability at high-resolutions. However, ‘over-sharpening’ due to the application of a single global B-factor can distort processed maps causing connected densities to appear broken and disconnected. This issue limits the interpretability of cryo-EM maps, i.e.ab initiomodelling. In this work, we propose 1) approaches to enhance high-resolution features of cryo-EM maps, while preventing map distortions and 2) methods to obtain local B-factors and electron density occupancy maps. These algorithms have as common link the use of the spiral phase transformation and are called LocSpiral, LocBSharpen, LocBFactor and LocOccupancy. Our results, which include improved maps of recent SARS-CoV-2 structures, show that our methods can improve the interpretability and analysis of obtained reconstructions.
DNA ligases ofProchlorococcus marinus: an evolutionary exception to the rules of replication
Authors: Hjerde Erik , Maguren Ashleigh , Rzoska-Smith Elizabeth , Kirby Bronwyn , Williamson Adele 
Published: May 2020

AbstractDNA ligases, essential enzymes which re-join the backbone of DNA come in two structurally-distinct isoforms, NAD-dependent and ATP-dependent, which differ in cofactor usage. The present view is that all bacteria exclusively use NAD-dependent DNA ligases for DNA replication, while archaea and eukaryotes use ATP-dependent DNA ligases. Some bacteria also possess auxiliary ATP-dependent DNA ligases; however, these are only employed for specialist DNA repair processes. Here we show that in the genomes of high-light strains of the marine cyanobacteriumProchlorococcocus marinus, an ATP-dependent DNA ligase has replaced the NAD-dependent form, overturning the present paradigm of a clear evolutionary split in ligase usage. Genes encoding partial NAD-dependent DNA ligases are found on mobile regions in highlight genomes and lack domains required for catalytic function. This constitutes the first reported example of a bacterium that relies on an ATP-dependent DNA ligase for DNA replication and recommendsP. marinusas a model to investigate the evolutionary origins of these essential DNA-processing enzymes.
Hematopoietic progenitors polarize in contact with bone marrow stromal cells by engaging CXCR4 receptors
Authors: Bessy Thomas , Souquet Benoit , Vianay Benoit , Schaeffer Alexandre , Jaffredo Thierry , Larghero Jerome , Blanchoin Laurent , Brunet Stephane , Faivre Lionel , Théry Manuel 
Published: May 2020

AbstractHematopoietic stem and progenitor cells (HSPCs) are located in the bone marrow, where they regulate the permanent production and renewal of all blood-cell types. HSPC proliferation and differentiation is locally regulated by their interaction with cells forming specific microenvironments close to the bone matrix or close to blood vessels. However, the cellular mechanisms underlying HSPC’s interaction with these cells and their potential impact on HSPC polarity is still poorly understood. Here we modelled the bone-marrow niche using microfluidic technologies in a bone-marrow on a chip device, and evaluated long-duration cell-cell contacts between single HSPCs and stromal cells or endothelial cells in a custom-designed microwell cell-culture system. We found that an HSPC can form a discrete contact site that leads to the extensive polarization of their cytoskeleton architectures. As in the case with immune synapses formed by lymphocytes, the centrosome was located in proximity of the cell-cell contact. The entire microtubule network emanated from the centrosome, and the nucleus was confined to the side opposite of the cell-cell contact. The capacity of the HSPC to polarize appeared specific as it was not observed in contact with skin fibroblasts. The receptors ICAM, VCAM and CXCR4 were identified in the polarizing contact, and were all independently capable of inducing morphological polarization. However, only CXCR4 was independently capable of inducing the polarization of the centrosome-microtubule network. Altogether these results revealed a novel mechanism of HSPC polarization associated with its anchorage to specific cells in the bone-marrow, which might be instrumental in the regulation of their fate.
Root specific plasticity induced by paclobutrazol confers improved deficit irrigation tolerance and agronomic performance in maize
Authors: Urfan Mohammad , Hakla Haroon Rashid , Sharma Shubham , Khajuria Manu , Satbhai Santosh B. , Vyas Dhiraj , Bhougal Sunil , Yadav Narendra Singh , Pal Sikander 
Published: May 2020

AbstractDrought stress in maize often results in poor growth and reduced yield. Antioxidants play vital role in management of abiotic stresses. Drought or water deficit are detrimental to young seedlings establishment and transition from vegetative to reproductive growth in maize. Paclobutrazol (PBZ) has been widely used to confer abiotic stress tolerance in plants, however, its impact on root developmental attributes in maize and their relevance in drought management are least understood. Comprehensive experiments over a three year period (2017-2019) under early deficit (EDI) and terminal deficit (TDI) irrigation with or without paclobutrazol (PBZ) were conducted on five maize varieties (DDKL, DKC-9144, PG-2475, PG-2320 and Bio-9621). Plant shoot and root growth kinetics, phenological changes and physiological perturbations including antioxidant profile coupled with molecular regulation of root traits, showed DKC-9144 as best variety in terms of plant fitness and reproductive performance under deficit irrigation. Root developmental rates were key contributors towards improved plant biomass and cob yield under deficit irrigation tolerance. Structural equation modelling (SEM) demonstrated specific contribution of different root types (crown, brace and seminal roots) in maize towards improving water use efficiency, cob yield and plant height. From SEM, seminal root surface area and root length are proposed desired traits to improve water use efficiency and cob yield in DKC-9144 under deficit irrigation. Bi-variate analyses of twenty key traits of plant fitness and agronomic importance showed a strong correlation (r) between root traits and improved growth performance and yield stability indices.
Cereulide synthetase acquisition and loss events within the evolutionary history of Group IIIBacillus cereus sensu latofacilitate the transition between emetic and diarrheal foodborne pathogen
Authors: Carroll Laura M. , Wiedmann Martin 
Published: May 2020

AbstractCereulide-producing members ofBacillus cereus sensu lato(B. cereus s.l.) Group III, also known as “emeticB. cereus”, possess cereulide synthetase, a plasmid-encoded, non-ribosomal peptide synthetase encoded by thecesgene cluster. Despite the documented risks that cereulide-producing strains pose to public health, the level of genomic diversity encompassed by “emeticB. cereus” has never been evaluated at a whole-genome scale. Here, we employ a phylogenomic approach to characterize Group IIIB. cereus s.l.genomes which possessces(ces-positive) alongside their closely relatedces-negative counterparts to (i) assess the genomic diversity encompassed by “emeticB. cereus”, and (ii) identify potentialcesloss and/or gain events within the evolutionary history of the high-risk and medically relevant sequence type (ST) 26 lineage often associated with emetic foodborne illness. Using all publicly availableces-positive Group IIIB. cereus s.l.genomes and theces-negative genomes interspersed among them (n= 150), we show that “emeticB. cereus” is not clonal; rather, multiple lineages within Group III harbor cereulide-producing strains, all of which share a common ancestor incapable of producing cereulide (posterior probability [PP] 0.86-0.89). The ST 26 common ancestor was predicted to have emerged asces-negative (PP 0.60-0.93) circa 1904 (95% highest posterior density [HPD] interval 1837.1-1957.8) and first acquired the ability to produce cereulide before 1931 (95% HPD 1893.2-1959.0). Three subsequentcesloss events within ST 26 were observed, including among isolates responsible forB. cereus s.l.toxicoinfection (i.e., “diarrheal” illness).Importance“B. cereus” is responsible for thousands of cases of foodborne disease each year worldwide, causing two distinct forms of illness: (i) intoxication via cereulide (i.e., “emetic” syndrome) or (ii) toxicoinfection via multiple enterotoxins (i.e., “diarrheal” syndrome). Here, we show that “emeticB. cereus” is not a clonal, homogenous unit that resulted from a single cereulide synthetase gain event followed by subsequent proliferation; rather, cereulide synthetase acquisition and loss is a dynamic, ongoing process that occurs across lineages, allowing some Group IIIB. cereus s.l.populations to oscillate between diarrheal and emetic foodborne pathogen over the course of their evolutionary histories. We also highlight the care that must be taken when selecting a reference genome for whole-genome sequencing-based investigation of emeticB. cereus s.l.outbreaks, as some reference genome selections can lead to a confounding loss of resolution and potentially hinder epidemiological investigations.
Active disturbance rejection control strategy for airborne radar stabilization platform based on cascade extended state observer
Authors: Mei Dong , Yu Zhu-Qing 
Published: May 2020

Purpose
This paper aims to improve the anti-interference ability of the airborne radar stabilization platform, especially the ability to suppress continuous disturbance under complex air conditions to ensure the clarity and stability of airborne radar imaging.

Design/methodology/approach
This paper proposes a new active disturbance rejection control (ADRC) strategy based on the cascade extended state observer (ESO) for airborne radar stabilization platform, which adopts two first-order ESOs to estimate the angular velocity value and the angular position value of the stabilized platform. Then makes the error signal which subtracts the estimated value of ESO from the output signal of the tracking-differentiator as the input signal of the nonlinear state error feedback (NLSEF), and according to the output signal of the NLSEF and the value which dynamically compensated the total disturbances estimated by the two ESO to produce the final control signal.

Findings
The simulation results show that, compared with the classical ADRC, the ADRC based on the cascade ESO not only estimates the unknown disturbance more accurately but also improves the delay of disturbance observation effectively due to the increase of the order of the observer. In addition, compared with the classical PID control and the classical ADRC, it has made great progress in response performance and anti-interference ability, especially in the complex air conditions.

Originality/value
The originality of the paper is the adoption of a new ADRC control strategy based on the cascade ESO to ameliorate the anti-interference ability of the airborne radar stabilization platform, especially the ability to suppress continuous interference under complex air conditions.
Practical implementation of 4D-trajectories in air traffic management: system requirements and time windows monitoring
Authors: Rodríguez-Sanz Álvaro , Claramunt Puchol Cecilia , Pérez-Castán Javier A. , Gómez Comendador Fernando , Arnaldo Valdés Rosa M. 
Published: May 2020

Purpose
The current air traffic management (ATM) operational approach is changing; “time” is now integrated as an additional fourth dimension on trajectories. This notion will impose on aircraft the compliance of accurate arrival times over designated checkpoints (CPs), called time windows (TWs). This paper aims to clarify the basic requirements and foundations for the practical implementation of this functional framework.

Design/methodology/approach
This paper reviews the operational deployment of 4D trajectories, by defining its relationship with other concepts and systems of the future ATM and communications, navigation and surveillance (CNS) context. This allows to establish the main tools that should be considered to ease the application of the 4D-trajectories approach. This paper appraises how 4D trajectories must be managed and planned (negotiation, synchronization, modification and verification processes). Then, based on the evolution of a simulated 4D trajectory, the necessary corrective measures by evaluating the degradation tolerances and conditions are described and introduced.

Findings
The proposed TWs model can control the time tolerance within less than 100 s along the passing CPs of a generic trajectory, which is in line with the expected future ATM time-performance requirements.

Originality/value
The main contribution of this work is the provision of a holistic vision of the systems and concepts that will be necessary to implement the new 4D-trajectory concept efficiently, thus enhancing performance. It also proposes tolerance windows for trajectory degradation, to understand both when an update is necessary and what are the conditions required for pilots and air traffic controllers to provide this update.
Cash crops financing, agricultural performance and sustainability: evidence from Nigeria
Authors: Asaleye Abiola John , Alege Philip O. , Lawal Adedoyin Isola , Popoola Olabisi , Ogundipe Adeyemi A. 
Published: May 2020

PurposeOne of the challenging factors in achieving sustainable growth is the inability of the Nigerian government to diversify the country's revenue base. This study aims to investigate the relationship between cash crop financing and agricultural performance in Nigeria.Design/methodologyFour crops were considered, namely, cotton, cocoa, groundnut and palm oil. The impact of cash crop finance shock on agricultural performance was investigated using the vector error correction model (VECM), while the long-run relationship was examined through the identification of long-run restrictions on the VECM.FindingsThe variance decomposition showed that financing shock is more sensitive to cause variation in aggregate employment than aggregate agricultural output in palm oil, while for cocoa, cotton and groundnut showed otherwise. The long-run structural equations exert a positive relationship between cash crop financing and agricultural performance, except for oil palm and cocoa financing that has a negative connection with agrarian employment.Research limitations/implicationsThe study is limited to the unavailability of data for agriculture sector capital utilisation, which was not used.Practical implicationsThese results show that long-run benefit can be maximised by appropriate funding in cotton and groundnut production to promote sustainable growth.Originality/valueThe study examines the impact of cash crop financing on agricultural performance with the aim to promote sustainable growth in Nigeria using identified VECM.
Competitive intelligence and strategy formulation: connecting the dots
Authors: Cavallo Angelo , Sanasi Silvia , Ghezzi Antonio , Rangone Andrea 
Published: May 2020

PurposeThis paper aims to examine how competitive intelligence (CI) relates to the strategy formulation process of firms.Design/methodology/approachDue to the novelty of the phenomenon and to the depth of the investigation required to grasp the mechanisms and logics of CI, a multiple case study has been performed related to four companies located in Brazil that adopted CI practices within dedicated business units to inform and support strategic decision-making.FindingsThe authors provide detailed empirical evidence on the connection and use of CI practices throughout each stage of the strategy formulation process. Moreover, the study suggests that CI practices, despite their strategic relevance and diffusion, are still extensively adopted for tactical use.Originality/valueThis study sheds light on how CI practices may inform, support, and be integrated in the strategy formulation process, as few studies have done before.
A three-phase interpenetrating continua approach for wave and porous structure interaction
Authors: Yang Liang , Buchan Andrew , Pavlidis Dimitrios , Jones Alan , Smith Paul , Sakai Mikio , Pain Christopher 
Published: May 2020

Purpose
This paper aims to propose a three-phase interpenetrating continua model for the numerical simulation of water waves and porous structure interaction.

Design/methodology/approach
In contrast with one-fluid formulation or multi-component methods, each phase has its own characteristics, density, velocity, etc., and each point is occupied by all phases. First, the porous structure is modelled as a phase of continua with a penalty force adding on the momentum equation, so the conservation of mass is guaranteed without source terms. Second, the adaptive unstructured mesh modelling with P1DG-P1 elements is used here to decrease the total number of degree of freedom maintaining the same order of accuracy.

Findings
Several benchmark problems are used to validate the model, which includes the Darcy flow, classical collapse of water column and water column with a porous structure. The interpenetrating continua model is a suitable approach for water wave and porous structure interaction problem.

Originality/value
The interpenetrating continua model is first applied for the water wave and porous structure interaction problem. First, the structure is modelled as phase of non-viscous fluid with penalty force, so the break of the porous structure, porosity changes can be easily embedded for further complex studies. Second, the mass conservation of fluids is automatically satisfied without special treatment. Finally, adaptive anisotropic mesh in space is employed to reduce the computational cost.