bluuebunny/crossref_metadata_2025_split huggingface dataset:
Correlative SMLM and electron tomography reveals endosome nanoscale domains
Authors: Franke Christian , Repnik Urska , Segeletz Sandra , Brouilly Nicolas , Kalaidzidis Yannis , Verbavatz Jean-Marc , Zerial Marino 
Published: May 2019

AbstractMany cellular organelles, including endosomes, show compartmentalization into distinct functional domains, which however cannot be resolved by diffraction-limited light microscopy. Single molecule localization microscopy (SMLM) offers nanoscale resolution but data interpretation is often inconclusive when the ultrastructural context is missing. Correlative light electron microscopy (CLEM) combining SMLM with electron microscopy (EM) enables correlation of functional sub-domains of organelles in relation to their underlying ultrastructure at nanometer resolution. However, the specific demands for EM sample preparation and the requirements for fluorescent single-molecule photo-switching are opposed. Here, we developed a novel superCLEM workflow that combines triple-colour SMLM (dSTORM & PALM) and electron tomography using semi-thin Tokuyasu thawed cryosections. We applied the superCLEM approach to directly visualize nanoscale compartmentalization of endosomes in HeLa cells. Internalized, fluorescently labelled Transferrin and EGF were resolved into morphologically distinct domains within the same endosome. We found that the small GTPase Rab5 is organized in nano-domains on the globular part of early endosomes. The simultaneous visualization of several proteins in functionally distinct endosomal sub-compartments demonstrates the potential of superCLEM to link the ultrastructure of organelles with their molecular organization at nanoscale resolution.SynopsisSuborganelle compartmentalization cannot be resolved by diffraction limited light microscopy and not interpreted without knowledge of the underlying ultrastructure. This work shows a novel superCLEM workflow that combines multi-colour single-molecule localization-microscopy with electron tomography to map several functional domains on early endosomes. superCLEM reveals that the small GTPase Rab5 is organized in nano-domains largely devoid from cargo molecules Transferrin and EGF and opens new possibilities to perform structure-function analysis of organelles at the nanoscale.
Distinct Spiking Patterns of Excitatory and Inhibitory Neurons and LFP Oscillations in Prefrontal Cortex during Sensory Discrimination
Authors: Tseng Hua-an , Han Xue 
Published: May 2019

AbstractPrefrontal cortex (PFC) spike activity and local field potential (LFP) oscillation dynamics are broadly linked to various aspects of behavior. PFC neurons can encode the identity of sensory stimuli and related behavioral outcome in a range of sensory discrimination tasks. However, it remains largely unclear how different neuron subtypes and related LFP oscillation features are modulated in mice during sensory discrimination. To understand how excitatory and inhibitory neurons in PFC are selectively engaged during sensory discrimination and how they relate to LFPs oscillations, we used tetrode devices to probe well isolated individual PFC neurons, and LFP oscillations, in mice performing a three-choice auditory discrimination task. We found that a majority of the PFC neurons, 78% of a total of 711 individual neurons, exhibited sensory evoked responses that are context and task-progression dependent. Using spike waveforms, we classified these responsive neurons into excitatory and inhibitory neurons, and found that both neuron subtypes were transiently modulated, with individual neurons’ responses peaking throughout the entire task duration. While the number of responsive excitatory neurons remain largely constant throughout the task, an increasing fraction of inhibitory neurons were gradually recruited as trial progressed. Further examination of the coherences between individual neurons and LFPs revealed that inhibitory neurons in general exhibit higher spike-field coherence with LFP oscillations than excitatory neurons, first at higher gamma frequencies at the beginning of the task, and then at theta frequencies during the task, and finally across theta, beta and gamma frequencies at task completion. Together, our results demonstrate that while PFC excitatory neurons are continuously engaged during sensory discrimination, PFC inhibitory neurons are preferentially engaged as task progresses and selectively coordinated with distinct LFP oscillations. These results demonstrate increasing involvement of inhibitory neurons in shaping the overall PFC network dynamics as sensory discrimination progressed towards completion.
Distinct and overlapping functions ofMiscanthus sinensisMYB transcription factors SCM1 and MYB103 in lignin biosynthesis
Authors: Golfier Philippe , Unda Faride , Murphy Emily K. , Xie Jianbo , He Feng , Zhang Wan , Mansfield Shawn D. , Rausch Thomas , Wolf Sebastian 
Published: May 2019

AbstractCell wall recalcitrance is a major constraint for the exploitation of lignocellulosic biomass as renewable resource for energy and bio-based products. Transcriptional regulators of the lignin biosynthetic pathway represent promising targets for tailoring lignin content and composition in plant secondary cell walls. A wealth of research in model organisms has revealed that transcriptional regulation of secondary cell wall formation is orchestrated by a hierarchical transcription factor (TF) network with NAC TFs as master regulators and MYB factors in the lower tier regulators. However, knowledge about the transcriptional regulation of lignin biosynthesis in lignocellulosic feedstocks, such as Miscanthus, is limited. Here, we characterized two Miscanthus MYB TFs, MsSCM1 and MsMYB103, and compared their transcriptional impact with that of the master regulator MsSND1. In Miscanthus leavesMsSCM1andMsMYB103are expressed at growth stages associated with lignification. Ectopic expression ofMsSCM1andMsMYB103in tobacco leaves was sufficient to trigger secondary cell wall deposition with distinct sugar and lignin composition. Moreover, RNA-seq analysis revealed that the transcriptional responses toMsSCM1andMsMYB103overexpression showed extensive overlap with the response toMsSND1, but were distinct from each other, underscoring the inherent complexity of secondary cell wall formation. Together,MsSCM1andMsMYB103represent interesting targets for manipulations of lignin content and composition in Miscanthus towards tailored biomass.
Gene Sets Analysis using Network Patterns
Authors: Linkowski Gregory , Blatti Charles , Kalari Krishna , Sinha Saurabh , Vasudevan Shobha 
Published: May 2019

ABSTRACTHigh throughput assays allow researchers to identify sets of genes related to experimental conditions or phenotypes of interest. These gene sets are frequently subjected to functional interpretation using databases of gene annotations. Recent approaches have extended this approach to also consider networks of gene-gene relationships and interactions when attempting to characterize properties of a gene set. We present here a supervised learning algorithm for gene set analysis, called ‘GeneSet MAPR’, that for the first time explicitly considers the patterns of direct as well as indirect relationships present in the network to quantify gene-gene similarities and then report shared properties of the gene set. Our extensive evaluations show that GeneSet MAPR performs better than other network-based methods for the task of identifying genes related to a given gene set, enabling more reliable functional characterizations of the gene set. When applied to the set of response-associated genes from a triple negative breast cancer study, GeneSet MAPR uncovers gene families such as claudins, kallikreins, and collagen type alpha chains related to patient’s response to treatment, and which are not uncovered with traditional analysis.
Base editing in Streptomyces with Cas9-deaminase fusions
Authors: Zhong Zhiyu , Guo Junhong , Deng Liang , Chen Li , Wang Jian , Li Sicong , Xu Wei , Deng Zixin , Sun Yuhui 
Published: May 2019

AbstractConventional CRISPR/Cas genetic manipulation has been profitably applied to the genus Streptomyces, the most prolific bacterial producers of antibiotics. However, its reliance on DNA double-strand break (DSB) formation leads to unacceptably low yields of desired recombinants. We have adapted for Streptomyces recently-introduced cytidine base editors (CBEs) and adenine base editors (ABEs) which enable targeted C-to-T or A-to-G nucleotide substitutions, respectively, bypassing DSB and the need for a repair template. We report successful genome editing in Streptomyces at frequencies of around 50% using defective Cas9-guided base editors and up to 100% by using nicked Cas9-guided base editors. Furthermore, we demonstrate the multiplex genome editing potential of the nicked Cas9-guided base editor BE3 by programmed mutation of nine target genes simultaneously. Use of the high-fidelity version of BE3 (HF-BE3) essentially improved editing specificity. Collectively, this work provides a powerful new tool for genome editing in Streptomyces.
Somatic cell nuclear transfer in non-enucleated goldfish oocytes: understanding DNA fate during meiosis resumption and first cellular division
Authors: Rouillon Charlène , Depincé Alexandra , Chênais Nathalie , Le Bail Pierre-Yves , Labbé Catherine 
Published: May 2019

AbstractNuclear transfer consists in injecting a somatic nucleus carrying valuable genetic information into a recipient oocyte to sire a diploid offspring who bears the genome of interest. It requires that the oocyte (maternal) DNA is removed. In fish, because enucleation is difficult to achieve, non-enucleated oocytes are often used and disappearance of the maternal DNA was reported in some clones. The present work explore which cellular events explain spontaneous erasure of maternal DNA, as mastering this phenomenon would circumvent the painstaking procedure of fish oocyte enucleation. The fate of the somatic and maternal DNA during meiosis resumption and first cell cycle was studied using DNA labeling and immunofluorescence in goldfish clones. Maternal DNA was always found as an intact metaphase within the oocyte, and polar body extrusion was minimally affected after meiosis resumption. During the first cell cycle, only 40 % of the clones displayed symmetric cleavage, and these symmetric clones contributed to 80 % of those surviving at hatching. Maternal DNA was often fragmented and located under the cleavage furrow. The somatic DNA was organized either into a normal mitotic spindle or abnormal multinuclear spindle. Scenarios matching the DNA behavior and the embryo fate are proposed.
Efficient phase coding in hippocampal place cells
Authors: Seenivasan Pavithraa , Narayanan Rishikesh 
Published: May 2019

ABSTRACTHippocampal place cells encode space through phase precession, whereby neuronal spike phase progressively advances during place-field traversals. What neural constraints are essential for achieving efficient transfer of information through such phase codes, while concomitantly maintaining signature neuronal excitability specific to individual cell types? We developed a conductance-based model for phase precession in CA1 pyramidal neurons within the temporal sequence compression framework, and defined phase-coding efficiency using information theory. We recruited an unbiased stochastic search strategy to build a model population that exhibited physiologically observed heterogeneities in intrinsic properties. Place-field responses elicited from these models matched signature sub- and supra-threshold place-cell characteristics, including phase precession, sub-threshold voltage ramps, increases in theta-frequency power and firing rate during place-field traversals. Employing this model population, we show that disparate parametric combinations with weak pair-wise correlations resulted in models with similar high-efficiency phase codes and similar excitability characteristics. Mechanistically, the emergence of such parametric degeneracy was dependent on the differential and variable impact of individual ion channels on phase-coding efficiency in different models, and importantly, on synergistic interactions between synaptic and intrinsic properties. Furthermore, our analyses predicted a dominant role for calcium-activated potassium channels in regulating phase precession and coding efficiency. Finally, change in afferent statistics, manifesting as input asymmetry, induced an adaptive shift in the phase code that preserved its efficiency, apart from introducing asymmetry in sub-threshold ramps and firing profiles during place-field traversals. Our study postulates degeneracy as a potential framework to attain the twin goals of efficient temporal coding and robust homeostasis.SIGNIFICANCE STATEMENTNeuronal intrinsic properties exhibit significant baseline heterogeneities, and change with activity-dependent plasticity and neuromodulation. How do hippocampal neurons encode spatial locations through the precise timings of their action potentials in the face of such heterogeneities? Here, employing a unifying synthesis of the temporal sequence compression, efficient coding and degeneracy frameworks, we show that there are several disparate routes for neurons to achieve high-efficiency spatial information transfer through such temporal codes. These disparate routes were consequent to the ability of neurons to produce precise encoding through distinct structural components, critically involving synergistic interactions between intrinsic and synaptic properties. Our results point to an explosion in the degrees of freedom available to a neuron in concomitantly achieving efficient coding and excitability homeostasis.
Single cell transcriptomics reveals opioid usage evokes widespread suppression of antiviral gene program
Authors: Karagiannis Tanya T. , Cleary John P. , Gok Busra , Martin Nicholas G. , Nelson Elliot C. , Cheng Christine S. 
Published: May 2019

AbstractChronic opioid usage not only causes addiction behavior through the central nervous system (CNS), but it also modulates the peripheral immune system. However, whether opioid usage positively or negatively impacts the immune system is still controversial. In order to understand the immune modulatory effect of opioids in a systematic and unbiased way, we performed single cell RNA sequencing (scRNA-seq) of peripheral blood mononuclear cells (PBMCs) from opioid-dependent individuals and non-dependent controls. We show that chronic opioid usage evokes widespread suppression of interferon-stimulated genes (ISGs) and antiviral gene program in naive monocytes and upon ex vivo stimulation with the pathogen component lipopolysaccharide (LPS) in multiple innate and adaptive immune cell types. Furthermore, scRNA-seq revealed the same phenomenon with in vitro morphine treatment; after just a short exposure to morphine stimulation, we observed the same suppression of antiviral genes in multiple immune cell types. These findings indicate that both acute and chronic opioid exposure may be harmful to our immune system by suppressing the antiviral gene program, our body’s defense response to potential infection. Our results suggest that further characterization of the immune modulatory effects of opioid use is critical to ensure the safety of clinical opioid usage.
Impact of project monitoring and evaluation practices on construction project success criteria in Ghana
Authors: Kissi Ernest , Agyekum Kofi , Baiden Bernard Kofi , Tannor Reuben Agyei , Asamoah George Effah , Andam Emmanuel Tweneboah 
Published: May 2019

Purpose
Monitoring and evaluation (M&E) of projects is a very important aspect of project execution and management. This is because proper M&E practices have a significant effect on the successful delivery of projects. The purpose of this paper is to examine the impact of project M&E practices on construction project success criteria.

Design/methodology/approach
Structured questionnaires were used to solicit the views of project professionals in the Ghanaian construction industry. The questions were developed through critical review of literature and complemented with a pilot interview on the subject. This paper utilized a partial least square–structural equation modeling (PLS–SEM) to establish the impact of project M&E practices (constructs) on project success based on the hypothesis.

Findings
Results showed that M&E practices had a positive statistical significant relationship with construction project success criteria. In addition, health and safety performance and project scope showed a strong significant relation with M&E practice, implying that, in developing countries, these two main constructs should be given critical attention in achieving project success.

Practical implications
The findings of this study may be useful to organizations in determining M&E techniques that are relevant and contribute highly to project success. This may go a long way to increase productivity and accelerate the rate of successful project delivery.

Originality/value
The application of rigorous analysis, PLS–SEM, gives a more reliable information on M&E practices that can ensure successful delivery of construction projects.
Using recurrence plots for stability analysis of ring-on-disc tribopairs
Authors: Sun Guodong , Zhu Hua , Ding Cong 
Published: May 2019

Purpose
AISI 52100-AISI 1045 specimens were used as the ring-on-disc tribopairs in the experiments to investigate the stability of friction process.

Design/methodology/approach
The coefficient of friction (COF) signals were measured throughout the friction process and the recurrence plots (RPs) and recurrence quantification analysis (RQA) are adapted to analyze the stability of the tribosystem.

Findings
The results show that the COF time-series acquired from different tests possess the same dynamic evolution laws. The evolution of RPs follows the rules of “disrupted-homogeneous-disrupted,” which corresponds to the “running-in, steady-state and increasing stages” of friction process. Additionally, the evolution laws of RQA measures LAM, Vmax and TT accord with the “bathtub curve.” Therefore, both RPs and RQA measures can inform quantitative interpretations of tribological behaviors and friction process identification.

Originality/value
The both RPs and RQA are capable of characterizing the tribological behaviors and can depict the various stages of friction process.
Improvement of lubrication performance of water lubricated polymer bearing via enlarged axial end bearing diameter
Authors: Lv Fangrui , Zou Donglin , Ta Na , Rao Zhu-Shi 
Published: May 2019

Purpose
The purpose of this paper is to improve the lubrication performance of a water-lubricated polymer bearing with axial grooves, especially enlarge the minimum film thickness.

Design/methodology/approach
The bearing diameter is enlarged near the axial ends of the journal, with axial openings of a trumpet shape. A numerical model is developed which considers the proposed trumpet-shaped openings, bush deformation and grooves. The generatrix of the trumpet-shaped opening is assumed to be a paraboloid. Three different variations are covered, and the influences of the trumpet-shaped openings’ parameters on the bearing performance are analyzed.

Findings
The appropriate trumpet-shaped openings at the axial ends effectively increase the minimum film thickness, and the impact of trumpet-shaped openings on load carrying capacity is very small or even negligible. For the water-lubricated polymer bearing with axial grooves analyzed in this paper, the appropriate trumpet-shaped openings increase the minimum film thickness from 0.53 to 11.14 µm and decrease the load carrying capacity by 2.48 per cent.

Practical implications
The results of this study can be applied to marine propeller shaft systems and other systems with polymer bearings.

Originality/value
This paper has presented an approach for significantly increasing the minimum film thickness of a water-lubricated polymer bearing. A study on the performance improvement of water-lubricated polymer bearings with axial grooves is of significant interest to the research community.
Mechanical design optimization of a series elastic actuator considering the control performance
Authors: Woo Hanseung , Kong Kyoungchul 
Published: May 2019

Purpose
Actuators for human-interactive robot systems require transparency and guaranteed safety. An actuation system is called transparent when it is able to generate an actuation force as desired without any actuator dynamics. The requirements for the transparent actuation include high precision and large frequency bandwidth in actuation force generation, zero mechanical impedance and so on. In this paper, a compact rotary series elastic actuator (cRSEA) is designed considering the actuation transparency and the mechanical safety.

Design/methodology/approach
The mechanical parameters of a cRSEA are optimally selected for the controllability, the input and output torque transmissibility and the mechanical impedance by simulation study. A mechanical clutch that automatically disengages the transmission is devised such that the human is mechanically protected from an excessive actuation torque due to any possible controller malfunction or any external impact from a collision. The proposed cRSEA with a mechanical clutch is applied to develop a wearable robot for incomplete paraplegic patients. To verify torque tracking performance and disengagement of the mechanical clutch, experiments were conducted.

Findings
As the effects of the gear ratio, N1, on the four control performance indexes are conflicting, it should be carefully selected such that the controllability and the output torque transmissibility are maximized, while the disturbance torque transmissibility and the mechanical impedance are minimized. When the four control performance indexes were equally weighted, N1 was selected as 30. Experimental results showed that the designed cRSEA provided good control performances and the mechanical clutch worked properly.

Originality/value
It is important to design the actuator so as to maximize the control performance in accordance with its purpose. This paper presents the design guidelines for the SEA by introducing four control performance indexes and analyzing how the performance indexes vary according to the change of design parameter. From the viewpoint of practicality, a mechanical clutch design method that prevents excessive torque from being transmitted to the wearer and an analysis to solve the locking phenomenon when using a worm gear are presented, and a design method of SEA satisfying both control performance and practicality is presented.