bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Computational Model of Bidirectional Axonal Growth in Micro-Tissue Engineered Neuronal Networks (micro-TENNs)
Authors: Marinov Toma , Yuchi Liang , Adewole Dayo O. , Cullen D. Kacy , Kraft Reuben H. 
Published: July 2018

AbstractMicro-Tissue Engineered Neural Networks (Micro-TENNs) are living three-dimensional constructs designed to replicate the neuroanatomy of white matter pathways in the brain, and are being developed as implantable microtissue for axon tract reconstruction or as anatomically-relevant in vitro experimental platforms. Micro-TENNs are composed of discrete neuronal aggregates connected by bundles of long-projecting axonal tracts within miniature tubular hydrogels. In order to help design and optimize micro-TENN performance, we have created a new computational model including geometric and functional properties. The model is built upon the three-dimensional diffusion equation and incorporates large-scale uni- and bi-directional growth that simulates realistic neuron morphologies. The model captures unique features of 3D axonal tract development that are not apparent in planar outgrowth, and may be insightful for how white matter pathways form during brain development. The processes of axonal outgrowth, branching, turning and aggregation/bundling from each neuron are described through functions built on concentration equations and growth time distributed across the growth segments. Once developed we conducted multiple parametric studies to explore the applicability of the method and conducted preliminary validation via comparisons to experimentally grown micro-TENNs for a range of growth conditions. Using this framework, this model can be applied to study micro-TENN growth processes and functional characteristics using spiking network or compartmental network modeling. This model may be applied to improve our understanding of axonal tract development and functionality, as well as to optimize the fabrication of implantable tissue engineered brain pathways for nervous system reconstruction and/or modulation.
Engrafted parenchymal brain macrophages differ from host microglia in transcriptome, epigenome and response to challenge
Authors: Shemer Anat , Grozovski Jonathan , Tay Tuan Leng , Tao Jenhan , Volaski Alon , Süß Patrick , Ardura-Fabregat Alberto , Gross-Vered Mor , Kim Jung-Seok , David Eyal , Chappell-Maor Louise , Thielecke Lars , Glass Christopher K. , Cornils Kerstin , Prinz Marco , Jung Steffen 
Published: July 2018

AbstractMicroglia are yolk sac-derived macrophages residing in the parenchyma of brain and spinal cord, where they interact with neurons and other glial cells by constantly probing their surroundings with dynamic extensions. Following different conditioning paradigms and bone marrow (BM) / hematopoietic stem cell (HSC) transplantation, graft-derived cells seed the brain and persistently contribute to the parenchymal brain macrophage compartment. Here we establish that these cells acquire over time microglia characteristics, including ramified morphology, longevity, radio-resistance and clonal expansion. However, even following prolonged CNS residence, transcriptomes and epigenomes of engrafted HSC-derived macrophages remain distinct from yolk sac-derived host microglia. Furthermore, BM graft-derived cells display discrete responses to peripheral endotoxin challenge, as compared to host microglia. Also in human HSC transplant recipients, engrafted cells remain distinct from host microglia, extending our finding to clinical settings. Collectively, our data emphasize the molecular and functional heterogeneity of parenchymal brain macrophages and highlight potential clinical implications for patients treated by HSC gene therapy.
Influence of Shea Tree (Vitellaria paradoxa) on Maize and Soybean Production
Authors: Ogwok Gertrude , Alele Peter O. , Kizza Sarah 
Published: July 2018

ABSTRACTVitellaria paradoxa provides many benefits to farmers within the Shea belt. However, increased threats to it necessitate its conservation, and one common approach is the practice of agroforestry. A number of studies have shown that Shea tree has influence on crop production, and yet, some of these studies were done using single season experiments or bioassays using mature Shea tree components. In this study, the seasonal influence of young and mature Shea trees on Maize and Soybean yields was investigated using field experiments in Otuke district of northern Uganda, where, Shea tree parklands are dominant and Maize and Soybean are used for food security and income. Our results show that there are differential responses of maize and soybean yield to rainy seasons and physiological differences of Vitellaria paradoxa treatment. We find yield reduction for maize more pronounced than yield reduction for soybeans under different Shea plants (Mature and Young) and for the two rainy seasons. We attribute the difference to the differential maize and soybean responses to Vitellaria paradoxa shading and its differential allelopathic inhibition of these crops. We recommend that Soybeans should be preferred to maize when planting under Shea canopy.
Accelerated detection of Gram negative bacteria in blood culture by enhanced acoustic flow cytometry (AFC) following peptide nucleic acid fluorescence in situ hybridization (PNA-FISH)
Authors: Huang Xiao Xuan , Urosevic Nadezda , Inglis Timothy J.J. 
Published: July 2018

AbstractBacteraemia is a risk factor for subsequent clinical deterioration and death. Current reliance on culture-based methods for detection of bacteraemia delays identification and assessment of this risk until after the optimal period for positively impacting treatment decisions has passed. Therefore, a method for rapid detection and identification of bacterial infection in the peripheral bloodstream in acutely ill patients is crucial for improved patient survival through earlier targeted antibiotic treatment. The turnaround time for current clinical laboratory methods ranges from 12 to 48 hours, emphasizing the need for a faster diagnostic test. Here we describe a novel assay for accelerated detection of bacterial infection in blood culture (BC) using peptide nucleic acid fluorescence in situ hybridization enhanced acoustic flow cytometry (PNA-FISH-AFC). For assay development, we used simulated blood cultures (BCs) spiked with one of three bacterial species: Escherichia coli, Klebsiella pneumoniae or Pseudomonas aeruginosa at a low concentration of 10 CFU/mL. Under current clinical settings, it takes a minimum of 12 hours incubation to reach positivity on the BacTEC system, corresponding to a bacterial concentration of 107-109 CFU/mL optimal for further analyses. In contrast, our PNA-FISH-AFC assay detected 103 – 104 CFU/mL bacteria in BC following a much shorter incubation of 5 to 10 hours in culture. Using either PCR-based FilmArray® assay or MALDI-TOF for bacterial detection, it took 7-10 and 12-24 hours of incubation, respectively, to reach the positive result. These findings indicate a potential time advantage of PNA-FISH-AFC assay over currently used laboratory techniques for rapid bacterial detection in BC with significantly improved turnaround time.
The finite state projection based Fisher information matrix approach to estimate information and optimize single-cell experiments
Authors: Fox Zachary , Munsky Brian 
Published: July 2018

AbstractModern optical imaging experiments not only measure single-cell and single-molecule dynamics with high precision, but they can also perturb the cellular environment in myriad controlled and novel settings. Techniques, such as single-molecule fluorescence in-situ hybridization, microfluidics, and optogenetics, have opened the door to a large number of potential experiments, which begs the question of how best to choose the best possible experiment. The Fisher information matrix (FIM) estimates how well potential experiments will constrain model parameters and can be used to design optimal experiments. Here, we introduce the finite state projection (FSP) based FIM, which uses the formalism of the chemical master equation to derive and compute the FIM. The FSP-FIM makes no assumptions about the distribution shapes of single-cell data, and it does not require precise measurements of higher order moments of such distributions. We validate the FSP-FIM against well-known Fisher information results for the simple case of constitutive gene expression. We then use numerical simulations to demonstrate the use of the FSP-FIM to optimize the timing of single-cell experiments with more complex, non-Gaussian fluctuations. We validate optimal simulated experiments determined using the FSP-FIM with Monte-Carlo approaches and contrast these to experiment designs chosen by traditional analyses that assume Gaussian fluctuations or use the central limit theorem. By systematically designing experiments to use all of the measurable fluctuations, our method enables a key step to improve co-design of experiments and quantitative models.Author summaryA main objective of quantitative modeling is to predict the behaviors of complex systems under varying conditions. In a biological context, stochastic fluctuations in expression levels among isogenic cell populations have required modeling efforts to incorporate and even rely upon stochasticity. At the same time, new experimental variables such as chemical induction and optogenetic control have created vast opportunities to probe and understand gene expression, even at single-molecule and single-cell precision. With many possible measurements or perturbations to choose from, researchers require sophisticated approaches to choose which experiment to perform next. In this work, we provide a new tool, the finite state projection based Fisher information matrix (FSP-FIM), which considers all cell-to-cell fluctuations measured in modern data sets, and can design optimal experiments under these conditions. Unlike previous approaches, the FSP-FIM does not make any assumptions about the shape of the distribution being measured. This new tool will allow experimentalists to optimally perturb systems to learn as much as possible about single-cell processes with a minimum of experimental cost or effort.
Base-pairing requirements for small RNA-mediated gene silencing of recessive self-incompatibility alleles inArabidopsis halleri
Authors: Burghgraeve N. , Simon S. , Barral S. , Fobis-Loisy I. , Holl A-C , Poniztki C. , Schmitt E. , Vekemans X. , Castric V. 
Published: July 2018

AbstractSmall non-coding RNAs are central regulators of genome activity and stability. Their regulatory function typically involves sequence similarity with their target sites, but understanding the criteria by which they specifically recognize and regulate their targets across the genome remains a major challenge in the field, especially in the face of the diversity of silencing pathways involved. The dominance hierarchy among self-incompatibility alleles in Brassicaceae is controlled by interactions between a highly diversified set of small non-coding RNAs produced by dominant S-alleles and their corresponding target sites on recessive S-alleles. By controlled crosses, we created numerous heterozygous combinations of S-alleles inArabidopsis halleriand developed an RT-qPCR assay to compare allele-specific transcript levels for the pollen determinant of self-incompatibility (SCR). This provides the unique opportunity to evaluate the precise base-pairing requirements for effective transcriptional regulation of this target gene. We found strong transcriptional silencing of recessiveSCRalleles in all heterozygote combinations examined. A simple threshold model of base-pairing for the sRNA-target interaction captures most of the variation inSCRtranscript levels. For a subset of S-alleles, we also measured allele-specific transcript levels of the determinant of pistil specificity (SRK) and found sharply distinct expression dynamics throughout flower development betweenSCRandSRK. In contrast toSCR, bothSRKalleles were expressed at similar levels in the heterozygote genotypes examined, suggesting no transcriptional control of dominance for this gene. We discuss the implications for the evolutionary processes associated with the origin and maintenance of the dominance hierarchy among self-incompatibility alleles.
Temporal and spatial asymmetries during stationary cycling cause different feedforward and feedback modifications in the muscular control of the lower limbs
Authors: Zych Magdalena , Rankin Ian , Holland Donal , Severini Giacomo 
Published: July 2018

AbstractMotor adaptations are useful for studying the way in which the lower limbs are controlled by the brain. However, motor adaptation paradigms for the lower limbs are typically based on locomotion tasks, where the necessity of maintaining postural stability is the main driver of adaptation and could possibly mask other underlying processes. In this study we investigated whether small temporal or spatial asymmetries can trigger motor adaptations during stationary cycling, where stability is not directly compromised. Fourteen healthy individuals participated in two experiments: in one of the experiments the angle between the crank arms of the pedals was altered by 10° to induce a temporal asymmetry; in the other the length of the right pedal was shortened by 2.4 cm to induce a spatial asymmetry. We recorded the acceleration of the crank arms and the EMG signals of 16 muscles (8 per leg). The analysis of the accelerometer data was used to investigate the presence of motor adaptations. Muscle synergy analysis was performed on each side to quantify changes in neuromuscular control. We found that feedforward motor adaptations are present in response to temporal asymmetries and are obtained by progressively shifting the activation patterns of two synergies on the right leg. Spatial asymmetries appear to trigger a feedback-driven response that does not present an aftereffect and is not consistent with a motor adaptation. This response is characterized by a step-like decrease in activity in the right gastrocnemius when the asymmetry is present and likely reflects the altered task demands.New and NoteworthyThe processes driving lower limb motor adaptations are not fully clear, and previous research appears to indicate that adaptations are mainly driven by stability. Here we show that lower limb adaptations can be obtained also in the absence of an explicit balance threat. We also show that adaptations are present also when kinematic error cannot be compensated for, suggesting the presence of intrinsic error measures regulating the timing of activation of the two legs.
Reaction diffusion plus growth: A numerical model for Turing morphogenesis and Ben-Jacob patterns
Authors: Trepka Kai 
Published: July 2018

ABSTRACTBuilding models of organismal growth enables predictions of natural variability and responses to perturbations. Complex systems such as animal pattern development and bacterial colonies can be modeled numerically using a reaction-diffusion system with relatively few factors and yield qualitatively accurate results, allowing exploration of different equilibrium and non-equilibrium solutions. Here, a discrete numerical reaction diffusion system is used to qualitatively reproduce both common animal patterns and Ben-Jacob bacterial growth.
Mild drought induces phenotypic and DNA methylation plasticity but no transgenerational effects in Arabidopsis
Authors: Van Dooren Tom JM , Bortolini Silveira Amanda , Gilbault Elodie , Jiménez-Gómez José M. , Martin Antoine , Bach Liên , Tisné Sébastien , Quadrana Leandro , Loudet Olivier , Colot Vincent 
Published: July 2018

SummaryWhether environmentally induced changes in phenotypes can be heritable is a topic with revived interest, in part because of observations in plants that heritable trait variation can occur without DNA sequence mutations. This other system of inheritance, called transgenerational epigenetics, typically involves differences in DNA methylation that are stable across multiple generations. However, it remains unknown if such a system responds to environmental changes and if it could therefore provide a rapid way for plants to generate adaptive heritable phenotypic variation. Here, we used a well-controlled phenotyping platform and whole-genome bisulfite sequencing to investigate potential heritable effects of mild drought applied over two successive generations in Arabidopsis thaliana. Plastic phenotypic responses were observed in plants exposed to drought. After an intervening generation without stress, descendants of stressed and non-stressed plants were phenotypically indistinguishable, except for very few trait-based parental effects, and irrespective of whether they were grown in control conditions or under water deficit. Moreover, while mild drought induced changes to the DNA methylome of exposed plants, DNA methylation variants were not inherited. These findings add to the growing body of evidence indicating that transgenerational epigenetics is not a common response of plants to environmental changes.
Drosophilaovarian germline stem cell cytocensor projections dynamically receive and attenuate BMP signaling
Authors: Wilcockson Scott G. , Ashe Hilary L. 
Published: July 2018

SUMMARYIn theDrosophilaovarian germline, BMP signals released by niche cells promote germline stem cell (GSC) maintenance. Although BMP signaling is known to repress expression of a key differentiation factor, it remains unclear whether BMP-responsive transcription also contributes positively to GSC identity. Here, we identify the GSC transcriptome using RNA-seq, including the BMP-induced transcriptional network. Based on these data, we provide evidence that GSCs form two types of cellular projections. Genetic manipulation and liveex vivoimaging reveal that both classes of projection allow GSCs to access a reservoir of Dpp held away from the GSC-niche interface. Moreover, microtubule-rich projections, termed ‘cytocensors’, form downstream of BMP and have additional functionality, which is to attenuate BMP signaling. In this way cytocensors allow dynamic modulation of signal transduction to facilitate differentiation following GSC division. This ability of cytocensors to attenuate the signaling response expands the repertoire of functions associated with signaling projections.
Creative Brains Show Reduced Mid Frontal Theta
Authors: Wokke Martijn E. , Padding Lisa , Ridderinkhof K. Richard 
Published: July 2018

AbstractCreativity is considered to be the driving force behind innovation and progress, yet the mechanisms supporting creative thought remain elusive. In the current study, we investigated whether fluctuations in top-down control are related to creative thinking. Here, participants performed a ‘caption this’ task in which they had to provide an original and apt caption to accompany a presented picture, while EEG signals were recorded. To assess changing levels of top-down control, we made use of the strong relationship between mid frontal oscillatory activity in the theta range (4-7 HZ) and top-down control. Results demonstrate that specifically during the process of optimization and implementation of creative solutions, lower levels of mid frontal theta resulted in higher levels of creativity. In addition, increased creativity related to enhanced functional connectivity between occipital and mid frontal cortex. Together, our findings indicate that creativity benefits from a top-down induced shift towards an internally-oriented state during idea optimization and evaluation.
Zika Virus Infection at Different Pregnancy Stages: Anatomopathological Findings, Target Cells and Viral Persistence in Placental Tissues
Authors: de Noronha Lucia , Zanluca Camila , Burger Marion , Suzukawa Andreia Akemi , Azevedo Marina , Rebutini Patricia Z. , Novadzki Iolanda Maria , Tanabe Laurina Setsuko , Presibella Mayra Marinho , Santos Claudia Nunes Duarte dos 
Published: July 2018

ABSTRACTZika virus (ZIKV) infection in humans has been associated with congenital malformations and other neurological disorders, such as Guillain-Barré syndrome. The mechanism(s) of ZIKV intrauterine transmission, the cell types involved, the most vulnerable period of pregnancy for severe outcomes from infection and other physiopathological aspects remain unknown. In this study, we analyzed placental samples obtained at the time of delivery from a group of twenty-four women diagnosed with ZIKV infection during the first, second or third trimesters of pregnancy. Villous immaturity was the main histological finding in the placental tissues, although placentas without alterations were also frequently observed. Significant enhancement of the number of syncytial sprouts was observed in the placentas of women infected during the third trimester, indicating the development of placental abnormalities after ZIKV infection. Hyperplasia of Hofbauer cells (HCs) was also observed in these third-trimester placental tissues, and remarkably, HCs were the only ZIKV-positive fetal cells found in the placentas studied that persisted until birth, as revealed by immunohistochemical (IHC) analysis. Thirty-three percent of women infected during pregnancy delivered infants with congenital abnormalities, although no pattern correlating the gestational stage at infection, the IHC positivity of HCs in placental tissues and the presence of congenital malformations at birth was observed. Placental tissue analysis enabled us to confirm maternal ZIKV infection in cases where serum from the acute infection phase was not available, which reinforces the importance of this technique in identifying possible causal factors of birth defects. The results we observed in the samples from naturally infected pregnant women may contribute to the understanding of some aspects of the pathophysiology of ZIKV.
Operational capabilities in an emerging country: quality and the cost trade-off effect
Authors: Scarpin Marcia Regina Santiago , Brito Luiz Artur Ledur 
Published: July 2018

PurposeThe purpose of this paper is to identify the operational capabilities in an emerging country, and to analyze the trade-off effect between the quality capability and the cost capability.Design/methodology/approachThe empirical data were drawn from 160 firms in Brazil. Scales were validated using the Q-sort method and confirmatory factor analysis. Different techniques were adopted to reduce common method variance. Data were analyzed using multiple line regression.FindingsThe results showed that quality has a positive relationship with delivery, flexibility, innovation and sustainability capabilities. However, it was not possible to observe a positive relationship between quality and cost that confirmed the presence of a trade-off between these two capabilities.Practical implicationsAn important practical contribution of this study is that it brings a new perspective to the relationship between quality and cost. Although quality is an important capability for the firm, emerging country managers need to understand that its implementation will take time and money; quality does not indicate an immediate reduction in cost.Originality/valueThis study helps expand research into operational capabilities in lesser-developed countries, such as Brazil. Most of the research on operational capabilities is conducted in industrialized countries. The paper also discusses the trade-off between the quality capability and cost capability. The results show that quality does not always lead to a reduction in cost.