bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transposable elements in individual genotypes ofDrosophila simulans
Authors: Signor Sarah 
Published: September 2019

AbstractTransposable elements are mobile DNA sequences that are able to copy themselves within a host’s genome. Within insects they often make up a substantial proportion of the genome. While they are the subject of intense research, often times when copy number is estimated it is estimated only at the population level, or in a limited number of individuals within a population. However, an important aspect of transposable element spread is the variance between individuals in activity. Do transposable elements accumulate at different rates in different genetic backgrounds? Using two populations ofDrosophila simulansfrom California and Africa I estimated transposable element copy number in individual genotypes. Some active transposable elements seem to be a property of the species, while others of the populations. I find that in addition to population level differences in transposable element load certain genotypes accumulate transposable elements at a much higher rate than others. Most likely active transposable elements are fairly rare, and were inherited only by specific genotypes that were used to create the inbred lines. Whether or not this reflects dynamics in natural populations, where transposable elements may accumulate in specific genotypes and maintain themselves in the population rather than being active at low levels population wide, is an open question.
Coordination amongst quadriceps muscles suggests neural regulation of internal joint stresses, not simplification of task performance
Authors: Alessandro Cristiano , Prashara Adarsh , Tentler David P. , Yeh Hsin-Yun , Barroso Filipe O. , Tresch Matthew C. 
Published: September 2019

SummaryMany studies have demonstrated co-variation between muscle activations during behavior, suggesting that muscles are not controlled independently. According to one common proposal, this co-variation reflects simplification of task performance by the nervous system, so that muscles with similar contributions to task variables are controlled together. Alternatively, this co-variation might reflect regulation of low-level aspects of movements that are common across tasks, such as stresses within joints. We examined these issues by analyzing co-variation patterns in quadriceps muscle activity during locomotion in rats. The three mono-articular quadriceps muscles (vastus medialis, VM; vastus lateralis, VL; vastus intermedius, VI) produce knee extension and so have identical contributions to task performance; the bi-articular rectus femoris (RF) produces an additional hip flexion. Consistent with the proposal that muscle co-variation is related to similarity of muscle actions on task variables, we found that the co-variation between VM and VL was stronger than their co-variations with RF. However, co-variation between VM and VL was also stronger than their co-variations with VI. Since all vastii have identical actions on task variables, this finding suggests that co-variation between muscle activity is not solely driven by simplification of task performance. Instead, the preferentially strong co-variation between VM and VL is consistent with the control of internal joint stresses: since VM and VL produce opposing mediolateral forces on the patella, the high positive correlation between their activation minimizes the net mediolateral patellar force. These results provide important insights into the interpretation of muscle co-variations and their role in movement control.
It’s about time: Analysing an alternative approach for reductionist modelling of linear pathways in systems biology
Authors: Korsbo Niklas , Jönsson Henrik 
Published: September 2019

AbstractThoughtful use of simplifying assumptions is crucial to make systems biology models tractable while still representative of the underlying biology. A useful simplification can elucidate the core dynamics of a system. A poorly chosen assumption can, however, either render a model too complicated for making conclusions or it can prevent an otherwise accurate model from describing experimentally observed dynamics.Here, we perform a computational investigation of linear pathway models that contain fewer pathway steps than the system they are designed to emulate. We demonstrate when such models will fail to reproduce data and how detrimental truncation of a linear pathway leads to detectable signatures in model dynamics and its optimised parameters.An alternative assumption is suggested for simplifying linear pathways. Rather than assuming a truncated number of pathway steps, we propose to use the assumption that the rates of information propagation along the pathway is homogeneous and instead letting the length of the pathway be a free parameter. This results in a three-parameter representation of arbitrary linear pathways which consistently outperforms its truncated rival and a delay differential equation alternative in recapitulating observed dynamics.Our results provide a foundation for well-informed decision making during model simplifications.1Author summaryMathematical modelling can be a highly effective way of condensing our understanding of biological processes and highlight the most important aspects of them. Effective models are based on simplifying assumptions that reduce complexity while still retaining the core dynamics of the original problem. Finding such assumptions is, however, not trivial.In this paper, we explore ways in which one can simplify long chains of simple reactions wherein each step is linearly dependent on its predecessor. After generating synthetic data from models that describe such chains in explicit detail, we compare how well different simplifications retain the original dynamics. We show that the most common such simplification, which is to ignore parts of the chain, often renders models unable to account for time delays. However, we also show that when such a simplification has had a detrimental effect, it leaves a detectable signature in its optimal parameter values. We also propose an alternative assumption which leads to a highly effective model with only three parameters. By comparing the effects of these simplifying assumptions in thousands of different cases and for different conditions we are able to clearly show when and why one is preferred over the other.
A qPCR assay for Bordetella pertussis cells that enumerates both live and dead bacteria
Authors: Ramkissoon Stacy , MacArthur Iain , Ibrahim Muktar , de Graaf Hans , Read Robert C. , Preston Andrew 
Published: September 2019

AbstractBordetella pertussis is the causative agent of whooping cough, commonly referred to as pertussis. Although the incidence of pertussis was reduced through vaccination, during the last thirty years it has returned to high levels in a number of countries. This resurgence has been linked to the switch from the use of whole-cell to acellular vaccines. Protection afforded by acellular vaccines appears to be short-lived compared to that afforded by whole cell vaccines. In order to inform future vaccine improvement by identifying immune correlates of protection, a human challenge model of B. pertussis colonisation has been developed. Accurate measurement of colonisation status in this model has required development of a qPCR-based assay to enumerate B. pertussis in samples that distinguishes between viable and dead bacteria. Here we report the development of this assay and its performance in the quantification of B. pertussis from human challenge model samples. This assay has future utility in diagnostic labs and in research where a quantitative measure of both B. pertussis number and viability is required.
Structure-Guided Mutagenesis Alters Deubiquitinating Activity and Attenuates Pathogenesis of a Murine Coronavirus
Authors: Deng Xufang , Chen Yafang , Mielech Anna M. , Hackbart Matthew , Kesely Kristina R. , Mettelman Robert C. , O’Brien Amornrat , Chapman Mackenzie E. , Mesecar Andrew D. , Baker Susan C. 
Published: September 2019

AbstractCoronaviruses express a multifunctional papain-like protease, termed PLP2. PLP2 acts as a protease that cleaves the viral replicase polyprotein, and a deubiquitinating (DUB) enzyme which removes ubiquitin moieties from ubiquitin-conjugated proteins. Previous in vitro studies implicated PLP2 DUB activity as a negative regulator of the host interferon (IFN) response, but the role of DUB activity during virus infection was unknown. Here, we used X-ray structure-guided mutagenesis and functional studies to identify amino acid substitutions within the ubiquitin-binding surface of PLP2 that reduced DUB activity without affecting polyprotein processing activity. We engineered a DUB mutation (Asp1772 to Ala) into a murine coronavirus and evaluated the replication and pathogenesis of the DUB mutant virus (DUBmut) in cultured macrophages and in mice. We found that the DUBmut virus replicates similarly as the wild-type virus in cultured cells, but the DUBmut virus activates an IFN response at earlier times compared to the wild-type virus infection in macrophages, consistent with DUB activity negatively regulating the IFN response. We compared the pathogenesis of the DUBmut virus to the wild-type virus and found that the DUBmut-infected mice had a statistically significant reduction (p<0.05) in viral titer in livers and spleens at day 5 post-infection, albeit both wild-type and DUBmut virus infections resulted in similar liver pathology. Overall, this study demonstrates that structure-guided mutagenesis aids the identification of critical determinants of PLP2-ubiquitin complex, and that PLP2 DUB activity plays a role as an interferon antagonist in coronavirus pathogenesis.ImportanceCoronaviruses employ a genetic economy by encoding multifunctional proteins that function in viral replication and also modify the host environment to disarm the innate immune response. The coronavirus papain-like protease 2 (PLP2) domain possesses protease activity, which cleaves the viral replicase polyprotein, and also DUB activity (de-conjugating ubiquitin/ubiquitin-like molecules from modified substrates) using identical catalytic residues. To separate the DUB activity from the protease activity, we employed a structure-guided mutagenesis approach and identified residues that are important for ubiquitin-binding. We found that mutating the ubiquitin-binding residues results in a PLP2 that has reduced DUB activity but retains protease activity. We engineered a recombinant murine coronavirus to express the DUB mutant and showed that the DUB mutant virus activated an earlier type I interferon response in macrophages and exhibited reduced pathogenesis in mice. The results of this study demonstrate that PLP2/DUB is an interferon antagonist and a virulence trait of coronaviruses.
Principles of 3D Nucleus Organization and Epigenetic Regulation in Diploid Genome Revealed by Multi-omic Data from Hybrid Mouse
Authors: Han Zhijun , Kairong Cui , Placek Katarzyna , Hong Ni , Lin Chengqi , Chen Wei , Zhao Keji , Jin Wenfei 
Published: September 2019

AbstractMost mammalian genomes are diploid and previous studies have extensively investigated the average epigenetic profiles of homologous chromosomes. Here we use hybrid mice to distinguish the epigenetic status and three-dimensional organization of homologous chromosomes. We generated Hi-C, ChIP-seq and RNA-seq datasets from CD4 T cells of B6, Cast and hybrid mice, respectively, and systematically analyzed the 3D nucleus organization and epigenetic regulation. Our data indicate that the inter-chromosomal interaction patterns between homologous chromosomes are similar and the similarity is highly correlated with their allelic co-expression levels. Construction of 3D nucleus based on allele-specific interaction frequency revealed symmetric positioning of homologous chromosomes in the 3D nuclear space. The inter-chromosomal interactions at centromeres are significantly weaker than those at telomeres, indicating positioning of centromeres toward the inside of chromosome territories and telomeres toward the surface of chromosome territories. The majority A|B compartments or topologically associated domains (TADs) are consistent between B6 and Cast. We found 58% of the haploids in hybrids maintain their parental compartment status at B6/Cast divergent compartments due to cis-effect. About 95% of the trans-effected B6/Cast divergent compartments converge to same compartment status potentially due to a shared cellular environment. We found the differentially expressed genes between the two haploids in hybrid were associated with either genetic associated cis-effects or epigenetic associated trans-effects. The widespread epigenetic differences between B6 and Cast suggest that epigenetic changes may be major contributors to differences between B6 and Cast. Our data revealed symmetrical positioning of homologous chromosomes in 3D nucleus and enhanced our understanding of allele-specific epigenetic regulation.
Clickable methionine as a universal probe for labelling intracellular bacteria
Authors: Atwal Sharanjeet , Giengkam Suparat , Jaiyen Yanin , Feaga Heather , Dworkin Jonathan , Salje Jeanne 
Published: September 2019

AbstractDespite their clinical and biological importance, the cell biology of obligate intracellular bacteria is less well understood than that of many free-living model organisms. One reason for this is that they are mostly genetically intractable. As a consequence, it is not possible to engineer strains expressing fluorescent proteins and therefore fluorescence light microscopy – a key tool in host-pathogen cell biology studies – is difficult. Strain diversity limits the universality of antibody-based immunofluorescence approaches. Here, we have developed a universal labelling protocol for intracellular bacteria based on a clickable methionine analog. Whilst we have applied this to obligate intracellular bacteria, we expect it to be useful for labelling free living bacteria as well as other intracellular pathogens.
Double asymmetric percolation drives a quadruple transition in sexual contact networks
Authors: Zheng Hongyu , Zeng Xiangrui 
Published: September 2019

AbstractSince 2007, ZIKV outbreaks have been occurring around the world. While ZIKV is mainly spread by mosquito vectors, transmission via sex activities enables the virus to spread in regions without mosquito vectors. Modeling the patterns of ZIKV outbreak in these regions remain challenging. We consider age as an asymmetric factor in transmitting ZIKV, in addition to gender as seen in previous literature, and modify the graph structure for better modeling of such patterns. We derived our results by both solving the underlying differential equations and simulation on population graph. Based on a double asymmetric percolation process on sexual contact networks. we discovered a quadruple ZIKV epidemic transition. Moreover, we explored the double asymmetric percolation on scale-free networks. Our work provides more insight into the ZIKV transmission dynamics through sexual contact networks, which may potentially provide better public health control and prevention means in a ZIKV outbreak.
Cytoskeletal organization in isolated plant cells under geometry control
Authors: Durand-Smet P. , Spelman Tamsin A. , Meyerowitz E. M. , Jönsson H. 
Published: September 2019

AbstractSpecific cell and tissue form is essential to support many biological functions of living organisms. During development, the creation of different shapes at the cellular and tissue level fundamentally requires the integration of genetic, biochemical and physical inputs.It is well established that the cortical microtubule network plays a key role in the morphogenesis of the plant cell wall by guiding the organisation of new cell wall material. Moreover, it has been suggested that light or mechanical stresses can orient the microtubules thereby controlling wall architecture and plant cell shape. The cytoskeleton is thus a major determinant of plant cell shape. What is less clear is how cell shape in turn influences cytoskeletal organization.Recent in vitro experiments and numerical simulations predicted that a geometry-based rule is sufficient to explain some of the microtubule organization observed in cells. Due to their high flexural rigidity and persistence length of the order of a few millimeters, MTs are rigid over cellular dimensions and are thus expected to align along their long axis if constrained in specific geometries. This hypothesis remains to be tested in cellulo.Here we present an experimental approach to explore the relative contribution of geometry to the final organization of actin and microtubule cytoskeletons in single plant cells. We show that, in cells constrained in rectangular shapes, the cytoskeleton align along the long axis of the cells. By studying actin and microtubules in cells with the same system we show that while actin organisation requires microtubules to be present to align the converse is not the case. A model of self organizing microtubules in 3D predicts that severing of microtubules is an important parameter controlling the anisotropy of the microtubule network. We experimentally confirmed the model predictions by analysing the response to shape change in plant cells with altered microtubule severing dynamics. This work is a first step towards assessing quantitatively how cell geometry contributes to the control of cytoskeletal organization in living plant cells.
Impact of female directors on the board and foreign institutional investors on earning manipulation of Chinese listed companies
Authors: Sial Muhammad Safdar , Vo Xuan Vinh , Al-Haddad Lara , Trang Thao Nguyen 
Published: September 2019

Purpose
The purpose of this paper is to check the impact of female directors on the board and foreign institutional investors on earnings manipulation.

Design/methodology/approach
The data sample includes Chinese listed companies on the Shenzhen and Shanghai stock exchanges. The data are collected from China Stock Market and Accounting Research database covering the period from 2010 to 2017. The authors use a dynamic generalized method of moments in the study.

Findings
The findings show that the presence of female director on the board has a significant negative impact on both discretionary accruals and real earning management. However, the authors obtain different results for foreign institutional investor investors. This may be the result of myopia as the foreign institutional stockholders in Chinese companies are looking for quick profit encouraging management to manipulate earnings. the findings survive several robustness tests.

Originality/value
The authors expect the research results provide ample evidence about how female directors affects earnings manipulation, and also hope the research helps to understand how, in China, institutional ownership affects earnings manipulation.
Synchrony-city: Sarajevo in five acts and few intervals
Authors: Harrington Selma , Dimitrijevic Branka , Salama Ashraf M. 
Published: September 2019

Purpose
The purpose of this paper is to focus on Sarajevo, the capital of Bosnia and Herzegovina, giving a general overview of its urban context through five historical periods, as part of a research study on its modernist architectural heritage.

Design/methodology/approach
Designed to mimic the theatrical process which unfolds through acts and intervals, the paper combines literary, architectural, journalistic and historical sources, to sketch the key periods which characterise the city’s urban morphology.

Findings
The sequence of acts and intervals points to the dramatic historic inter-change of continuities and ruptures, in which the ruptures have often been less studied and understood. This explains the frequent conceptualising of Sarajevo through East–West binary, which synthesises it as a provincial capital from Ottoman and later Habsburg rule, a regional centre within two Yugoslav states and a capital city of a young state of Bosnia and Herzegovina. This highlights the need to study the ruptures as clues to the flow of continuities, in which the care and after care for built environment provide a field of evidence and possibilities for diverse perspectives of examination.

Research limitations/implications
Corroborated by secondary sources, the paper examines the accounts of urban heritage destruction in the 1990s war, as recorded by a writer, an architect and a journalist, and outlines a pattern of unbroken inter-relations between urban and architectural space (tangible) and sense and identity of place (intangible).

Practical implications
This discourse is relevant to the current situation where the city of Sarajevo expands again, in the complexity of a post-conflict society.

Social implications
Challenged by the political divisions and the laissez-faire economy, the public mood and interest is under-represented and has many conflicting voices.

Originality/value
Inspired by Italo Calvino’s Invisible Cities and the accounts from the siege of Sarajevo in the 1990s, this conceptual paper contributes to the formulation of a cross-disciplinary discursive prism through which the fragments of the city and its periods come together or apart, adding, subtracting and changing layers of meaning of the physical space.
Turbulent flows in a spiral double-pipe heat exchanger
Authors: Tian Zhe , Abdollahi Ali , Shariati Mahmoud , Amindoust Atefeh , Arasteh Hossein , Karimipour Arash , Goodarzi Marjan , Bach Quang-Vu 
Published: September 2019

Purpose
This paper aims to study the fluid flow and heat transfer through a spiral double-pipe heat exchanger. Nowadays using spiral double-pipe heat exchangers has become popular in different industrial segments due to its complex and spiral structure, which causes an enhancement in heat transfer.

Design/methodology/approach
In these heat exchangers, by converting the fluid motion to the secondary motion, the heat transfer coefficient is greater than that of the straight double-pipe heat exchangers and cause increased heat transfer between fluids.

Findings
The present study, by using the Fluent software and nanofluid heat transfer simulation in a spiral double-tube heat exchanger, investigates the effects of operating parameters including fluid inlet velocity, volume fraction of nanoparticles, type of nanoparticles and fluid inlet temperature on heat transfer efficiency.

Originality/value
After presenting the results derived from the fluid numerical simulation and finding the optimal performance conditions using a genetic algorithm, it was found that water–Al2O3 and water–SiO2 nanofluids are the best choices for the Reynolds numbers ranging from 10,551 to 17,220 and 17,220 to 31,910, respectively.
Numerical investigation of anguilliform locomotion by the SPH method
Authors: Rahmat Amin , Nasiri Hossein , Goodarzi Marjan , Heidaryan Ehsan 
Published: September 2019

Purpose
This paper aims to introduce a numerical investigation of aquatic locomotion using the smoothed particle hydrodynamics (SPH) method.

Design/methodology/approach
To model this problem, a simple improved SPH algorithm is presented that can handle complex geometries using updatable dummy particles. The computational code is validated by solving the flow over a two-dimensional cylinder and comparing its drag coefficient for two different Reynolds numbers with those in the literature.

Findings
Additionally, the drag coefficient and vortices created behind the aquatic swimmer are quantitatively and qualitatively compared with available credential data. Afterward, the flow over an aquatic swimmer is simulated for a wide range of Reynolds and Strouhal numbers, as well as for the amplitude envelope. Moreover, comprehensive discussions on drag coefficient and vorticity patterns behind the aquatic are made.

Originality/value
It is found that by increasing both Reynolds and Strouhal numbers separately, the anguilliform motion approaches the self-propulsion condition; however, the vortices show different pattern with these increments.