bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prenatal cadmium exposure does not induce greater incidence or earlier onset of autoimmunity in the offspring
Authors: McCall Jamie L. , Blair Harry C. , Blethen Kathryn E. , Hall Casey , Elliott Meenal , Barnett John B. 
Published: March 2021

AbstractWe previously demonstrated that exposure of adult mice to environmental levels of cadmium (Cd) alters the immune cell development and function with increases in anti-streptococcal antibody levels, as well as decreases in splenic natural regulatory T cells (nTreg) in the adult female offspring. Based on these data, we hypothesized that prenatal Cd exposure could predispose an individual to developing autoimmunity as adults. To test this hypothesis, the effects of prenatal Cd on the development of autoimmune diabetes and arthritis were investigated. Non-obese diabetic (NOD) mice were exposed to Cd in a manner identical to our previous studies, and the onset of diabetes was assessed in the offspring. Our results showed a similar time-to-onset and severity of disease to historical data, and there were no statistical differences between Cd-exposed and control offspring. Numerous other immune parameters were measured and none of these parameters showed biologically relevant differences between Cd-exposed and control animals. To test whether prenatal Cd-exposure affected development of autoimmune arthritis, we used SKG mice. While the levels of arthritis were similar between Cd-exposed and control offspring of both sexes, the pathology of arthritis determined by micro-computed tomography (μCT) between Cd-exposed and control animals, showed some statistically different values, especially in the female offspring. However, the differences were small and thus, the biological significance of these changes is open to speculation. Overall, based on the results from two autoimmune models, we conclude that prenatal exposure to Cd did not lead to a measurable propensity to develop autoimmune disease later in life.
An autoregulation loop infust-1for circular RNA regulation inCaenorhabditis elegans
Authors: Cao Dong 
Published: March 2021

AbstractCircular RNAs (circRNAs) are always expressed tissue-specifically, suggestive of specific factors that regulate their biogenesis. Here, taking advantage of available mutation strains of RNA binding proteins (RBPs) inCaenorhabditis elegans, I performed a screening of circRNA regulation in thirteen conserved RBPs. Among them, loss of FUST-1, the homolog of FUS (Fused in Sarcoma), caused downregulation of multiple circRNAs. By rescue experiments, I confirmed FUST-1 as a circRNA regulator. Further, I showed that FUST-1 regulates circRNA formation without affecting the levels of the cognate linear mRNAs. When recognizing circRNA pre-mRNAs, FUST-1 can affect both exon-skipping and circRNA in the same genes. Moreover, I identified an autoregulation loop infust-1, where FUST-1, isoform a promotes the skipping of exon 5 of its own pre-mRNA, which produces FUST-1, isoform b with different N-terminal sequences. FUST-1, isoform a is the functional isoform in circRNA regulation. Although FUST-1, isoform b has the same functional domains as isoform a, it cannot regulate either exon-skipping or circRNA formation.
Task-specific modulation of corticospinal neuron activity during skilled motor learning
Authors: Serradj Najet , Marino Francesca , Moreno-López Yunuen , Bernstein Amanda , Agger Sydney , Soliman Marwa , Sloan Andrew , Hollis Edmund 
Published: March 2021

AbstractThe learning of motor skills relies on plasticity of the primary motor cortex as task acquisition drives the remodeling of cortical motor networks1,2. Large scale cortical remodeling of evoked motor outputs occurs in response to the learning of skilled, corticospinal-dependent behavior, but not simple, unskilled tasks1. Here we determine the response of corticospinal neurons to both skilled and unskilled motor training and assess the role of corticospinal neuron activity in the execution of the trained behaviors. Usingin vivocalcium imaging, we found temporal coding of corticospinal activity coincided with the development of skilled, but not unskilled, motor expertise. Animals that failed to learn our skilled, precision isometric pull task exhibited a limited repertoire of dynamic movements and reduced network modulation. Transection of the corticospinal tract and optogenetic regulation of corticospinal activity show the necessity for patterned corticospinal network activity in the execution of skilled, but not unskilled, movement. We reveal a critical role for corticospinal network modulation in the learning and execution of skilled motor movements. The integrity of the corticospinal tract is essential to the recovery of dexterous movement after central nervous system injuries and these findings should help to shape translational approaches to motor recovery.
Functional diversity alters the effects of a pulse perturbation on the dynamics of tritrophic food webs
Authors: Ceulemans Ruben , Wojcik Laurie Anne , Gaedke Ursula 
Published: March 2021

AbstractBiodiversity decline causes a loss of functional diversity, which threatens ecosystems through a dangerous feedback loop: this loss may hamper ecosystems’ ability to buffer environmental changes, leading to further biodiversity losses. In this context, the increasing frequency of climate and human-induced excessive loading of nutrients causes major problems in aquatic systems. Previous studies investigating how functional diversity influences the response of food webs to disturbances have mainly considered systems with at most two functionally diverse trophic levels. Here, we investigate the effects of a nutrient pulse on the resistance, resilience and elasticity of a tritrophic—and thus more realistic—plankton food web model depending on its functional diversity. We compare a non-adaptive food chain with no diversity to a highly diverse food web with three adaptive trophic levels. The species fitness differences are balanced through trade-offs between defense/growth rate for prey and selectivity/half-saturation constant for predators. We showed that the resistance, resilience and elasticity of tritrophic food webs decreased with larger perturbation sizes and depended on the state of the system when the perturbation occured. Importantly, we found that a more diverse food web was generally more resistant, resilient, and elastic. Particularly, functional diversity dampened the probability of a regime shift towards a non-desirable alternative state. In addition, despite the complex influence of the shape and type of the dynamical attractors, the basal-intermediate interaction determined the robustness against a nutrient pulse. This relationship was strongly influenced by the diversity present and the third trophic level. Overall, using a food web model of realistic complexity, this study confirms the destructive potential of the positive feedback loop between biodiversity loss and robustness, by uncovering mechanisms leading to a decrease in resistance, resilience and elasticity as functional diversity declines.
LPS core type diversity in the Escherichia coli species and associations with phylogeny and virulence gene repertoire
Authors: Leclercq Sébastien , Branger Maxime , Smith David GE , Germon Pierre 
Published: March 2021

ABSTRACTEscherichia coli is a very versatile species for which diversity has been explored from various perspectives highlighting, for example, phylogenetic groupings, pathovars as well as a wide range of O serotypes. The highly variable O-antigen, the most external part of the lipopolysaccharide component of the outer membrane of E. coli, is linked to the innermost lipid A through the core region of LPS of which 5 different structures, denominated K-12, R1, R2, R3 and R4, have been characterized so far. The aim of the present study was to analyze the prevalence of these LPS core types in the E. coli species and explore their distribution in the different E. coli phylogenetic groups and in relationship with the virulence gene repertoire. Results indicated an uneven distribution of core types between the different phylogroups, with phylogroup A strains being the most diverse in terms of LPS core types while phylogroups B1, D and E strains were dominated by the R3 type and phylogroups B2 and C strains being dominated by the R1 type. Strains carrying the LEE virulence operon were mostly of the R3 type whatever the phylogroup while, within phylogroup B2, strains carrying a K-12 core all belonged to the complex STc131, one of the major clone of extra-intestinal pathogenic E. coli (ExPEC) strains. The origin of this uneven distribution is discussed but remains to be explained, as well as the consequences of carrying a specific core type on the physiology of the bacteria.IMPACT STATEMENTThe diversity of the E. coli species in terms of type of infections is well known, and its surface O-antigen which shows some correspondence to pathogenicity. This study is the first one to report in detail the diversity and distribution of the LPS core types in the E. coli species using whole genome sequences. This distribution of the 5 know core types is analyzed in the different phylogroups along with their association with specific virulence gene repertoire. Results indicate a non-random distribution of LPS core types in the E. coli species and, most interestingly, preferential association of certain core types with either some phylogenetic clades or with particular virulence gene repertoires. This work is a first step towards the identification of the origin of this diversity as well as towards the exploration of the physiological properties associated with specific core types.DATA SUMMARYComplete list of strains with associated data is available in supplementary table S1.
Population diversity of cassava mosaic begomoviruses increases over the course of serial vegetative propagation
Authors: Aimone Catherine D. , Lavington Erik , Hoyer J. Steen , Deppong David O. , Mickelson-Young Leigh , Jacobson Alana , Kennedy George G. , Carbone Ignazio , Hanley-Bowdoin Linda , Duffy Siobain 
Published: March 2021

AbstractCassava mosaic disease (CMD) represents a serious threat to cassava, a major root crop for more than 300 million Africans. CMD is caused by single-stranded DNA begomoviruses that evolve rapidly, making it challenging to develop durable disease resistance. In addition to the evolutionary forces of mutation, recombination, and reassortment, factors such as climate, agriculture practices, and the presence of DNA satellites may impact viral diversity. To gain insight into the factors that alter and shape viral diversityin planta, we used high-throughput sequencing to characterize the accumulation of nucleotide diversity after inoculation of infectious clones corresponding to African cassava mosaic virus (ACMV) and East African cassava mosaic Cameroon virus (EACMCV) in the susceptible cassava landrace Kibandameno. We found that vegetative propagation had a significant effect on viral nucleotide diversity, while temperature and a satellite DNA did not have measurable impacts in our study. EACMCV diversity increased linearly with the number of vegetative propagation passages, while ACMV diversity increased for a time and then decreased in later passages. We observed a substitution bias toward C→T and G→A for mutations in the viral genomes consistent with field isolates. Non-coding regions excluding the promoter regions of genes showed the highest levels of nucleotide diversity for each genome component. Changes in the 5’ intergenic region of DNA-A resembled the sequence of the cognate DNA-B sequence. The majority of nucleotide changes in coding regions were non-synonymous, most with predicted deleterious effects on protein structure, indicative of relaxed selection pressure over 6 vegetative passages. Overall, these results underscore the importance of knowing how cropping practices affect viral evolution and disease progression.
A chromosome-level genome assembly of the European Beech (Fagus sylvatica) reveals anomalies for organelle DNA integration, repeat content and distribution of SNPs
Authors: Mishra Bagdevi , Ulaszewski Bartosz , Meger Joanna , Aury Jean-Marc , Bodénès Catherine , Lesur-Kupin Isabelle , Pfenninger Markus , Silva Corinne Da , Gupta Deepak K , Guichoux Erwan , Heer Katrin , Lalanne Céline , Labadie Karine , Opgenoorth Lars , Ploch Sebastian , Provost Grégoire Le , Salse Jérôme , Scotti Ivan , Wötzel Stefan , Plomion Christophe , Burczyk Jaroslaw , Thines Marco 
Published: March 2021

AbstractThe European Beech is the dominant climax tree in most regions of Central Europe and valued for its ecological versatility and hardwood timber. Even though a draft genome has been published recently, higher resolution is required for studying aspects of genome architecture and recombination. Here we present a chromosome-level assembly of the more than 300 year-old reference individual, Bhaga, from the Kellerwald-Edersee National Park (Germany). Its nuclear genome of 541 Mb was resolved into 12 chromosomes varying in length between 28 Mb and 73 Mb. Multiple nuclear insertions of parts of the chloroplast genome were observed, with one region on chromosome 11 spanning more than 2 Mb of the genome in which fragments up to 54,784 bp long and covering the whole chloroplast genome were inserted randomly. Unlike inArabidopsis thaliana, ribosomal cistrons are present inFagus sylvaticaonly in four major regions, in line with FISH studies. On most assembled chromosomes, telomeric repeats were found at both ends, while centromeric repeats were found to be scattered throughout the genome apart from their main occurrence per chromosome. The genome- wide distribution of SNPs was evaluated using a second individual from Jamy Nature Reserve (Poland). SNPs, repeat elements and duplicated genes were unevenly distributed in the genomes, with one major anomaly on chromosome 4. The genome presented here adds to the available highly resolved plant genomes and we hope it will serve as a valuable basis for future research on genome architecture and for understanding the past and future of European Beech populations in a changing climate.
Revealing Notch-dependencies in synaptic targets associated with Alzheimer’s disease
Authors: Perna A. , Marathe S. , Dreos R. , Falquet L. , Akarsu H. , Auber L. Alberi 
Published: March 2021

AbstractAlzheimer’s disease (AD) is a progressive neurodegenerative disorder and the major cause of dementia. There is evidence that synaptic dysfunction and perturbation of Excitatory/Inhibitory (E/I) balance arise at the early stages of AD, altering the normal neural network activity, and leading to cognitive decline. Recent studies have identified Notch signaling as a contributor of neurodegenerative advancement including AD pathophysiology. As part of the efforts to understand molecular mechanisms and players involved in cognitive decline, we employed transgenic mouse models with Notch1 and RBPJK loss of function (LOF) in pyramidal neurons of the CA fields. Using bulk RNAseq. We have investigated the differential expression of Notch-dependent genes either upon environmental enrichment (EE) or upon Kainate injury (KA). We found a substantial genetic diversity in absence of both Notch1 receptor or Rbpjk transcriptional activator. Among differentially expressed genes, we observed a significant upregulation of Gabra2a in both knockout models, suggesting a role for Notch signaling in the modulation of E/I balance. Upon neuroexcitotoxic stimulation, loss of Rbpjk results in decreased expression of synaptic proteins with neuroprotective effects. We confirmed Nptx2, Npy, Pdch8, TncC as direct Notch1/Rbpjk targets and Bdnf and Scg2 as indirect targets. Finally, we translate these findings into human entorhinal cortex containing the hippocampal region from Alzheimer’s Disease patients performing targeted transcripts analysis. We observe an increased trend for Rbpjk and the ligand DNER but not Notch1 expression. On the other hand, neuron-specific targets, Nptx2, Npy, BDNF and Gabra2a are upregulated during the mild-moderate stage, and decline in the severe phase of the disease. These findings identify Notch as a promising signaling cascade to fine-tune in order to ameliorate synaptic transmission and memory deficits that occur during early phase of the Alzheimer’s Disease.HighlightsLoss of canonical and/or non-canonical Notch1 signaling in pyramidal neurons of the hippocampal CA field mainly affects the post-synaptic compartment.In both RBPJKcKO and Notch1cKO mouse models there is upregulation of GABAergic receptor subunit alpha2 (Gabra2a).The plasticity genes: Npy, Nptx2,Pcdh8 and TncC with neuroprotective functions and known association with Alzheimer’s Disease are direct Notch/Rbpjk targets.During the mild-moderate stage of AD dementia, Notch canonical signaling promotes the expression of neuroprotective proteins, in the attempt of mitigating the effect of the excitatory-inhibitory imbalance. This activity is not observed during severe stages of the disease.
Fluid-structure interaction computational analysis and experiments of tsunami bore forces on coastal bridges
Authors: Mazinani Iman , Sarafraz Mohammad Mohsen , Ismail Zubaidah , Hashim Ahmad Mustafa , Safaei Mohammad Reza , Wongwises Somchai 
Published: March 2021

Purpose
Two disastrous Tsunamis, one on the west coast of Sumatra Island, Indonesia, in 2004 and another in North East Japan in 2011, had seriously destroyed a large number of bridges. Thus, experimental tests in a wave flume and a fluid structure interaction (FSI) analysis were constructed to gain insight into tsunami bore force on coastal bridges.

Design/methodology/approach
Various wave heights and shallow water were used in the experiments and computational process. A 1:40 scaled concrete bridge model was placed in mild beach profile similar to a 24 × 1.5 × 2 m wave flume for the experimental investigation. An Arbitrary Lagrange Euler formulation for the propagation of tsunami solitary and bore waves by an FSI package of LS-DYNA on high-performance computing system was used to evaluate the experimental results.

Findings
The excellent agreement between experiments and computational simulation is shown in results. The results showed that the fully coupled FSI models could capture the tsunami wave force accurately for all ranges of wave heights and shallow depths. The effects of the overturning moment, horizontal, uplift and impact forces on a pier and deck of the bridge were evaluated in this research.

Originality/value
Photos and videos captured during the Indian Ocean tsunami in 2004 and the 2011 Japan tsunami showed solitary tsunami waves breaking offshore, along with an extremely turbulent tsunami-induced bore propagating toward shore with significantly higher velocity. Consequently, the outcomes of this current experimental and numerical study are highly relevant to the evaluation of tsunami bore forces on the coastal, over sea or river bridges. These experiments assessed tsunami wave forces on deck pier showing the complete response of the coastal bridge over water.
MHD flows on irregular boundary over a diverging channel with viscous dissipation effect
Authors: G. Iyyappan , Singh Abhishek Kumar 
Published: March 2021

Purpose
The purpose of this paper is to analyse the force convection laminar boundary layer flow on irregular boundary in diverging channel with the presence of magnetic field effects. Effects of various fluid parameters such as suction/injection, viscous dissipation, magnetic parameter and heat source/sink on velocity and temperature profiles are numerically analyzed. Moreover, numerically investigated on skin-friction and heat transfer coefficients when suction/injection occur.

Design/methodology/approach
The governing coupled partial differential equations are transformed to dimensionless form using non-similarity transformations. The non-dimensional partial differential equations are linearized by quasi-linearization technique and solved by varga's algorithm with numerical finite difference scheme on a non-uniform mesh.

Findings
The computation results are presented in terms of temperature, heat transfer and skin friction coefficients; these are useful for determining surface heat requirements. It was found that, in finite difference scheme for non-uniform mesh with quasi-linearization technique method gives smoothness of solution compared to finite difference scheme for uniform mesh, and this evidence is graphically represented in Figure 2.

Originality/value
The impacts of viscous dissipation (Ec) and magnetic parameter (Ha) on temperature profiles, skin friction and heat transfer are analyzed, which determine the heat generation/absorption to ensure the MHD flow of the laminar boundary layer on irregular boundary over a diverging channel.
A comparative study of urban resilience in coping with the crisis in the metropolises of Tehran and Mashhad
Authors: Nedaei Amin , Seyednaghavi Mirali , Firouzfar Marzieh , Zamani Nahid 
Published: March 2021

PurposeIn recent years, cities have been facing economic, social and environmental crises that need to be prevented and dealt with. The new subject that has been brought up to improve city resistance to crises is urban resilience. The purpose of this study is to compare the resilience of Tehran and Mashhad to identify the strengths and weaknesses of these two cities for better planning in critical situations.Design/methodology/approachThe research methodology is a comparative survey. The importance of the subject was manifested through a literature review. A questionnaire is designed using “the Rockefeller Foundation and ARUP’s model” and the Delphi method for testing 21 research hypotheses to evaluate resilience in the two cities (12 Delphi questionnaires and 232 urban resilience questionnaires). The data is analyzed using independent samplest-test by SPSS software.FindingsThe results show that both the cities are weak in terms of resilience indicators and sub-indicators, but Mashhad is more resilient than Tehran.Originality/valueThis paper compares urban resilience in Iran for the first time through a comparative study between two metropolises in the country. The Delphi method also is used for the first time (in Iranian case studies) to obtain the dimensions of urban resilience. By comparing the two cities, we can better understand their strengths and weaknesses.
Dynamic framework of performance assessment for startups
Authors: Antunes Luiz Guilherme Rodrigues , Vasconcelos Fernando Freire , Oliveira Camila Maria de , Corrêa Hamilton Luiz 
Published: March 2021

PurposeThe purpose of this paper is to develop a performance evaluation framework designed exclusively to look at startups' reality.Design/methodology/approachThis paper is exclusively theoretical, however, with the application of the Delphi method. For the application of this method, the framework was transformed in a questionnaire with closed- and open-ended questions, which is applied to 12 experts in this theme. A pre-test of the instrument was carried out, and the analysis was developed by sum.FindingsAs a result, the framework presents a cyclic format, encompassing the strategy, goal, modules, indicators, actions and evaluation of the performance assessment method, using a spiral format, and assigning the time variable.Research limitations/implicationsThis research contributes for the advance of performance assessment methods that consider organizations' life cycle and for the assessment of startups, for presenting an exclusive tool in this context.Practical implicationsThe results can contribute as a potential management tool with an integrative, recursive and continuous character. It has the potential to imply the behavior and capabilities of managers, given their difficulties in managing their business.Originality/valueAs originality of the work, the use of the organization life cycle stands out to compose a performance evaluation process, which has not yet been addressed in the performance literature.