bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bac-PULCE: Bacterial Strain and AMR Profiling Using Long Reads via CRISPR Enrichment
Authors: Sajuthi Andrea , White Julia , Ferguson Gayle , Freed Nikki E. , Silander Olin K. 
Published: October 2020

AbstractRapid identification of bacterial pathogens and their antimicrobial resistance (AMR) profiles is critical for minimising patient morbidity and mortality. While many sequencing methods allow deep genomic and metagenomic profiling of samples, widespread use (for example atpoint-of-care settings) is impeded because substantial sequencing and computational infrastructure is required for sequencing and analysis. Here we present Bac-PULCE (Bacterial strain and antimicrobial resistance Profiling Using Long reads via CRISPR Enrichment), which combines CRISPR-cas9 based targeted sequence enrichment with long-read sequencing. We show that this method allows simultaneous bacterial strain-level identification and antimicrobial resistance profiling of single isolates or metagenomic samples with minimal sequencing throughput. In contrast to short read sequencing, long read sequencing used in Bac-PULCE enables strain-level resolution even when targeting and sequencing highly conserved genomic regions, such as 16S rRNA. We show that these long reads allow sequencing of additional AMR genes linked to the targeted region. Additionally, long reads can be used to identify which species in a metagenomic sample harbour specific AMR loci. The ability to massively multiplex crRNAs suggests that this method has the potential to substantially increase the speed and specificity of pathogen strain identification and AMR profiling, while ensuring low computational overhead.ImportanceThere is a critical need for rapid and identification of bacterial strains and antibiotic resistance profiles in clinical settings. However, most current methods require both substantial laboratory infrastructure (e.g. for DNA sequencing), substantial compute infrastructure (e.g. for bioinformatic analyses), or both. Here we present a new method, Bac-PULCE, (Bacterial strain and antimicrobial resistance Profiling Using Long reads via CRISPR Enrichment), which combines CRISPR-cas9 based targeted sequence enrichment with long-read sequencing on the Oxford Nanopore platform. This allows rapid profiling of bacterial strains and antibiotic resistance genes in a sample while requiring very little laboratory or computational infrastructure.
Early-life feeding accelerates gut microbiome maturation in piglets
Authors: Choudhury R. , Middelkoop A. , Gerrits W.J.J. , Kemp B. , Bolhuis J.E. , Kleerebezem M. 
Published: October 2020

ABSTRACTEarly-life microbiome perturbations have been suggested to have important effects on host development, physiology, and behaviour, which can persist throughout life. We hypothesise that early feeding (access to a pre-weaning fibrous diet) can affect gut microbiome colonisation and development in neonatal piglets. In this longitudinal study, a customised fibrous diet was provided to early-fed piglets (EF; 6 litters) starting two days after birth until weaning (28 days of age) in addition to mother’s milk, whereas control piglets (CON; 4 litters) suckled sow’s milk only. Rectal swabs were collected at multiple timepoints until six weeks of age (i.e., 2 weeks post-weaning) to investigate intestinal microbiota composition development over time using 16S rRNA gene profiling (n = 10 piglets per treatment). We observed a dynamic intestinal microbiota colonisation pattern during the pre-weaning period in both treatment groups, which rapidly stabilised within 2 weeks post-weaning. The microbial (alpha) diversity increased with age and seemed to reach a plateau in the early post-weaning time-point (day+5). The homogenous post-weaning microbiota was represented by microbial groups includingPrevotella, Roseburia, Faecalibacterium, Ruminococcus, Megasphaera, CatenibacteriumandSubdoligranulum. Remarkably, early feeding of neonatal piglets resulted in accelerated maturation of the intestinal microbiota at pre-weaning time-points, characterised by increased rate of microbial diversity and expanded colonisation of typical post-weaning associated microbial groups (mentioned above) at pre-weaning stages. The acceleration in EF piglets was illustrated by the simultaneous emergence of typical post-weaning-associated microbial groups and a more rapid decline of typical early-life/pre-weaning microbial genera. In addition, the individual eating behaviour scores of the piglets quantitatively correlated with the accelerated change of their microbiome. Overall, these findings show the importance of early-life nutritional strategies to influence the gut microbiota maturation in piglets.
Checkpoint inhibition of origin firing prevents inappropriate replication outside of S-phase
Authors: Johnson Mark C. , Can Geylani , Santos Miguel , Alexander Diana , Zegerman Philip 
Published: October 2020

AbstractAcross eukaryotes, checkpoints maintain the order of cell cycle events in the face of DNA damage or incomplete replication. Although a wide array of DNA lesions activates the checkpoint kinases, whether and how this response differs in different phases of the cell cycle remains poorly understood. The S-phase checkpoint for example results in the slowing of replication, which in the budding yeastSaccharomyces cerevisiaeis caused by Rad53 kinase-dependent inhibition of the initiation factors Sld3 and Dbf4. Despite this, we show here that Rad53 phosphorylates both of these substrates throughout the cell cycle at the same sites as in S-phase, suggesting roles for this pathway beyond S-phase. Indeed we show that Rad53-dependent inhibition of Sld3 and Dbf4 limits re-replication in G2/M phase, preventing inappropriate gene amplification events. In addition we show that inhibition of Sld3 and Dbf4 after DNA damage in G1 phase prevents premature replication initiation at all origins at the G1/S transition. This study redefines the scope and specificity of the ‘S-phase checkpoint’ with implications for understanding the roles of this checkpoint in the majority of cancers that lack proper cell cycle controls.
Reproductive resilience but not root architecture underpin yield improvement in maize (Zea maysL.)
Authors: Messina Carlos , Cooper Mark , McDonald Dan , Poffenbarger Hanna , Clark Randy , Salinas Andrea , Fang Yinan , Gho Carla , Tang Tom , Graham Geoff 
Published: October 2020

AbstractPlants capture soil resources to produce the grains required to feed a growing population. Because plants capture water and nutrients through roots, it was proposed that changes in root systems architecture (RSA) underpin the three-fold increase in maize grain yield over the last century1,2,3,4. Within this framework, improvements in reproductive resilience due to selection are caused by increased water capture1. Here we show that both root architecture and yield have changed with decades of maize breeding, but not the water capture. Consistent with Darwinian agriculture5theory, improved reproductive resilience6,7enabled farmers increase the number of plants per unit land8,9,10, capture soil resources, and produced more dry matter and grain. Throughout the last century, selection operated to adapt roots to crowding, enabling reallocation of C from large root systems to the growing ear and the small roots of plants cultivated in high plant populations in modern agriculture.
Engineering lithoheterotrophy in an obligate chemolithoautotrophic Fe(II) oxidizing bacterium
Authors: Jain Abhiney , Gralnick Jeffrey A. 
Published: October 2020

ABSTRACTNeutrophilic Fe(II) oxidizing bacteria likeMariprofundus ferrooxydansare obligate chemolithoautotrophic bacteria that play an important role in the biogeochemical cycling of iron and other elements in multiple environments. These bacteria generally exhibit a singular metabolic mode of growth which prohibits comparative “omics” studies. Furthermore, these bacteria are considered non-amenable to classical genetic methods due to low cell densities, the inability to form colonies on solid medium, and production of copious amounts of insoluble iron oxyhydroxides as their metabolic byproduct. Consequently, the functional understanding of these bacteria remains speculative despite the availability of substantial genomic information. Here we develop the first genetic system in neutrophilic Fe(II) oxidizing bacterium and use it to engineer lithoheterotrophy inM. ferrooxydans, a metabolism that has been speculated but not experimentally validated. Our work suggests thatM. ferroxydanspartitions energy generation from carbon oxidation. This synthetic biology approach could be extended to gain physiological understanding and domesticate other bacteria that grow using a single metabolic mode.
TransMPRA: A framework for assaying the role of manytrans-acting factors at many enhancers
Authors: Calderon Diego , Ellis Andria , Daza Riza M. , Martin Beth , Tome Jacob M. , Chen Wei , Chardon Florence M. , Leith Anh , Lee Choli , Trapnell Cole , Shendure Jay 
Published: October 2020

AbstractGene regulation occurs throughtrans-acting factors (e.g.transcription factors) acting oncis-regulatory elements (e.g.enhancers). Massively parallel reporter assays (MPRAs) functionally survey large numbers ofcis-regulatory elements for regulatory potential, but do not identify thetrans-acting factors that mediate any observed effects. Here we describetransMPRA — a reporter assay that efficiently combines multiplex CRISPR-mediated perturbation and MPRAs to identifytrans-acting factors that modulate the regulatory activity of specific enhancers.
On-campus student accommodation safety measures: provision versus risk analysis
Authors: Simpeh Fredrick , Adisa Solomon 
Published: October 2020

PurposeThis paper compares the provision and risk associated with the lack of safety measures in the student accommodations of a university in the Western Cape province, South Africa, with the aim of developing a guide to improve the provision of the safety measures.Design/methodology/approachThe study adopted a case study research strategy. A questionnaire was used as an instrument to collect quantitative data, whereas an interview was conducted to collect qualitative data. Both descriptive (mean score) and inferential (pairedt-test) statistics were used to analyse the quantitative data, whereas a content analysis was used to analyse the qualitative data.FindingsAlthough most of the measures were provided, few critical measures were not adequate or not provided at all. Moreover, the mean scores obtained indicated that there were statistically significant differences between the provision and risk of non-provision of most of the measures. Weapon detector, closed-circuit television (CCTV), water sprinkler system, lift for disabled students, disabled toilet facility, burglar bar on doors, first aid box, medically trained personnel on post and accident logbook were identified as measures requiring urgent attention.Research limitations/implicationsData were collected only from one university; therefore, the findings of the research study may not be generalised. Thus, a study that can expand the number of participating universities is recommended.Practical implicationsThe facilities department and safety unit can use the recommendations provided to improve the safety of the student accommodations. Policymakers could also benefit from the findings of the study.Originality/valueThere is dearth of studies focussing mainly on student accommodation security and safety measures from the infrastructure point of view. Thus, this article contributes to the body of knowledge in this area.
Bitcoin, VIX futures and CDS: a triangle for hedging the international equity portfolios
Authors: Zghal Rania , Ghorbel Ahmed 
Published: October 2020

PurposeIn this paper, our aim is to estimate the time varying correlations between Bitcoin, VIX futures and CDS indexes and to examine in what ways these assets can act as beneficial hedge and safe haven mechanisms, useful for facing, or attenuating, the major world equity markets related risks and volatilities.Design/methodology/approachOur methodology consists to model each pair equity/asset indices by bivariate symmetric and asymmetric dynamic conditional models (A) DCC to evaluate the portfolio design associated implications on both daily and weekly collected data base, with regard to the period ranging from July, 2010 to January 2018. To assess the extent to which the Bitcoin, VIX futures and sovereign CDS may stand as diversifiers, i.e. as hedging or safe haven instruments against the various stock indexes, we adopt the same method applied by Baur and Lucey (2010).FindingsEmpirical results show that the hedging and safe haven roles associated with the three hedging instruments tend to differ noticeably across time horizons and model used. The interest brought about by treating this issue is twofold. On the one hand, it should provide useful guidelines to investors through helping them opt for the most effective and beneficial strategies, whereby they could efficiently hedge the equity markets related extreme risks and volatilities. On the other hand, it is intended to highlight the applied models' specifications associated impacts.Research limitations/implicationsThe interest brought about by treating this issue is twofold. On the one hand, it should provide useful guidelines to investors and financial advisors through helping them opt for the most effective and beneficial of the strategies, whereby they could efficiently hedge the equity markets related extreme risks and volatilities. On the other hand, it is intended to highlight the applied models' specifications associated impacts.Originality/valueStudy of Bitcoin can be considered as safe haven or hedge or diversifier instrument. Compare between Bitcoin, VIX and CDs.
Static modeling and analysis of soft manipulator considering environment contact based on segmented constant curvature method
Authors: Chen Yinglong , Li Wenshuo , Gong Yongjun 
Published: October 2020

Purpose
The purpose of this paper is to estimate the deformation of soft manipulators caused by obstacles accurately and the contact force and workspace can be also predicted.

Design/methodology/approach
The continuum deformation of the backbone of the soft manipulator under contact is regarded as two constant curvature arcs and the curvatures are different according to the fluid pressure and obstacle location based on piecewise constant curvature framework. Then, this study introduces introduce the moment balance and energy conservation equation to describe the static relationship between driving moment, elastic moment and contact moment. Finally, simulation and experiments are carried out to verify the accuracy of the proposed model.

Findings
For rigid manipulators, environmental contact except for the manipulated object was usually considered as a “collision” which should be avoided. For soft manipulators, an environment is an important tool for achieving manipulation goals and it might even be considered to be a part of the soft manipulator’s end-effector in some specified situations.

Research limitations/implications
There are also some limitations to the presented study. Although this paper has made progress in the static modeling under environmental contact, some practical factors still limit the further application of the model, such as the detection accuracy of the environment location and the deformation of the contact surface.

Originality/value
Based on the proposed kinematic model, the bending deformation with environmental contact is discussed in simulations and has been experimentally verified. The comparison results show the correctness and accuracy of the presented SCC model, which can be applied to predict the slender deformation under environmental contact without knowing the contact force.
COVID-19 pandemic and economic crisis: the Nigerian experience and structural causes
Authors: Ozili Peterson K. 
Published: October 2020

PurposeThis paper analyses the COVID-19 situation in Nigeria, its effect on the economy and the structural causes that worsened the coronavirus (COVID-19) crisis.Design/methodology/approachThis paper uses simple descriptive analysis to examine the COVID-19 situation in Nigeria.FindingsThe findings reveal that the economic downturn in Nigeria was triggered by a combination of declining oil price and spillovers from the COVID-19 outbreak, which not only led to a fall in the demand for oil products but also stopped economic activities from taking place when social distancing policies were enforced. The government responded to the crisis by providing financial assistance to businesses and a small number of households that were affected by the coronavirus (COVID-19) outbreak. The monetary authority adopted accommodative monetary policies and offered a targeted 3.5 trillion loan support to some sectors. These efforts should have prevented the economic crisis from occurring but it did not. Economic agents could not freely engage in economic activities for fear of contracting the COVID-19 disease that was spreading very fast at the time.Practical implicationsThe implication of the study is that policymakers should pay attention to three areas of the economy for economic and structural reform. One, policymakers should introduce economic reforms to diversify the economy and reduce Nigeria's dependence on revenue from crude oil export. Two, policymakers in Nigeria should invest in healthcare infrastructure to improve the ability of the national health system to withstand the outbreak of contagious diseases. Three, there is also a need to build appropriate digital infrastructure to facilitate the transition from “face-to-face” business activities to a “digital or online” business activities, which can help to grow the digital economy. Also, policymakers should use legislation to create a robust social welfare safety net for all citizens particularly for unemployed citizens and poor households.Originality/valueThis is the first paper that looks at the economic implication of COVID-19 in a West African country.
How does the cryptocurrency market affect the stock market performance in the MENA region?
Authors: Sami Mina , Abdallah Wael 
Published: October 2020

PurposeThis paper examines the impact of cryptocurrency market on the stock market performance in Middle East and North Africa (MENA) region. A comparative analysis is extended to distinguish this impact between Gulf countries and other economies in the region.Design/methodology/approachThe analysis uses the information of cryptocurrencies and the stock market indices of the Gulf countries for the period 2014–2018 on a daily basis. Two strategies have been implemented to fulfill the goal of the study: first, the tests strategy, which is applied using the cointegration analysis and panel-specific forms of Granger causality; second, the regression strategy, which is applied mainly using the instrument variable with generalized method of moments (IV-GMM) method.FindingsThe results show that there is a significant relationship between the cryptocurrency market and the stock market performance in the MENA region. On the one hand, for the Gulf countries that claim full obedience to the Islamic Sharia rules, each 1% increase in the cryptocurrency returns reduces the stock market performance by 0.15%. On the other hand, for the non-Gulf (other MENA) countries that have flexibility in applying the Islamic Sharia rules or do not follow it, the stock market performance increases by 0.13%, for each 1% increase in the cryptocurrency returns.Originality/valueThe paper proposes two main contributions: First, the paper introduces the cryptocurrency returns as one of the determinants of the stock market performance in the MENA region. This impact is distinguished based on the degree of applying the Islamic Sharia rules and the vision of the government to the stock market. Second, the paper provides an empirical guideline for governments in the MENA region for efficient measures in their stock market, given the important expansion of the cryptocurrency market and the government type.
Business model innovation and growth of manufacturing SMEs: a social exchange perspective
Authors: Chen Jiawen , Liu Linlin , Wang Yong 
Published: October 2020

PurposeThis study investigates business model innovation in small- and medium-sized manufacturing enterprises (SMEs) and its impact on firm growth.Design/methodology/approachThe study was based on analyzing data collected through a questionnaire survey. Structural equation modeling was applied to test the hypotheses.FindingsBusiness model innovation has a positive effect on SME growth in the manufacturing sectors. Moreover, growth is also achieved through the indirect effect of business model innovation on customer trust and commitment.Practical implicationsManagers will benefit from understanding how business model innovation can help their companies to overcome resource constraints and achieve sustained growth. When manufacturing SMEs engage in modular or structural changes to their business model, they may find it worthwhile to focus on maintaining a relationship of trust and commitment with their customers.Originality/valueThis study highlights business model innovation as a unique and important, yet underexplored, factor in manufacturing SME growth. The findings also untangle the complex processes of customer relationship management by which business model innovation improves manufacturing competitive advantage for SMEs.