bluuebunny/crossref_metadata_2025 huggingface dataset:
FLASH: a next-generation CRISPR diagnostic for multiplexed detection of antimicrobial resistance sequences
Authors: Quan Jenai , Langelier Charles , Kuchta Alison , Batson Joshua , Teyssier Noam , Lyden Amy , Caldera Saharai , McGeever Aaron , Dimitrov Boris , King Ryan , Wilheim Jordan , Murphy Maxwell , Ares Lara Pesce , Travisano Katherine A , Sit Rene , Amato Roberto , Mumbengegwi Davis R , Smith Jennifer L , Bennett Adam , Gosling Roly , Mourani Peter M , Calfee Carolyn S , Neff Norma F , Chow Eric D , Kim Peter S , Greenhouse Bryan , DeRisi Joseph L , Crawford Emily D
Published: May 2019

The growing prevalence of deadly microbes with resistance to previously life-saving drug therapies is a dire threat to human health. Detection of low abundance pathogen sequences remains a challenge for metagenomic Next Generation Sequencing (NGS). We introduce FLASH (Finding Low Abundance Sequences by Hybridization), a next-generation CRISPR/Cas9 diagnostic method that takes advantage of the efficiency, specificity and flexibility of Cas9 to enrich for a programmed set of sequences. FLASH-NGS achieves up to 5 orders of magnitude of enrichment and sub-attomolar gene detection with minimal background. We provide an open-source software tool (FLASHit) for guide RNA design. Here we applied it to detection of antimicrobial resistance genes in respiratory fluid and dried blood spots, but FLASH-NGS is applicable to all areas that rely on multiplex PCR.
A Heterocyst-Specific Antisense RNA Contributes to Metabolic Reprogramming in Nostoc sp. PCC 7120
Authors: Olmedo-Verd Elvira , Brenes-�lvarez Manuel , Vioque Agust�n , Muro-Pastor Alicia M
Published: May 2019

Upon nitrogen deficiency, some filamentous cyanobacteria differentiate specialized cells, called heterocysts, devoted to N2 fixation. Heterocysts appear regularly spaced along the filaments and exhibit structural and metabolic adaptations, such as loss of photosynthetic CO2 fixation or increased respiration, to provide a proper microaerobic environment for its specialized function. Heterocyst development is under transcriptional control of the global nitrogen regulator NtcA and the specific regulator HetR. Transcription of a large number of genes is induced or repressed upon nitrogen deficiency specifically in cells undergoing differentiation. In recent years, the HetR regulon has been described to include heterocyst-specific trans-acting small RNAs and antisense RNAs (asRNAs), suggesting that there is an additional layer of post-transcriptional regulation involved in heterocyst development. Here, we characterize in the cyanobacterium Nostoc (Anabaena) sp. PCC 7120 an asRNA, that we call as_glpX, transcribed within the glpX gene encoding the Calvin cycle bifunctional enzyme sedoheptulose-1,7-bisphosphatase/fructose-1,6-bisphosphatase (SBPase). Transcription of as_glpX is restricted to heterocysts and is induced very early during the process of differentiation. Expression of as_glpX RNA promotes the cleavage of the glpX mRNA by RNase III, resulting in a reduced amount of SBPase. Therefore, the early expression of this asRNA could contribute to the quick shut-down of CO2 fixation in those cells in the filament that are undergoing differentiation into heterocysts. In summary, as_glpX is the first naturally occurring asRNA shown to rapidly and dynamically regulate metabolic transformation in Nostoc heterocysts. The use of antisense transcripts to manipulate gene expression specifically in heterocysts could became a useful tool for metabolic engineering in cyanobacteria.
Brassinosteroid Regulates Root Development with Highly Redundant Genes in Hexaploid Wheat
Authors: Hou Lijiang , Zhang Aihua , Wang Ruochen , Zhao Peng , Zhang Dongzhi , Jiang Yujie , Diddugodage Chamila Jeewani , Wang Xiaoming , Ni Zhongfu , Xu Shengbao
Published: May 2019

Brassinosteroid (BR) plays an important role in plant development and biotic and abiotic stress tolerance, but its specific function remains largely unknown in wheat (Triticum aestivum L.), preventing its utilization in this important crop. In this study, the function of BR and its underlying cytological role in wheat root development were comprehensively investigated. Our findings demonstrated that BR has a conserved function in regulating root length in wheat, and novel roles in regulating lateral root emergence and root diameter were uncovered. Analyses of BR homologous gene composition and evolutionary divergence demonstrated that the genetic framework of the wheat BR pathway was close to that of rice, but contained highly redundant homologous copies of genes from the subgenome A, B and D. These homologous copies showed active expression and shared a conserved BR response. The expression of wheat DWF4 and glycogen synthase kinase (GSK) genes in Arabidopsis confirmed that multiple homologous copies maintained their conserved function in regulating root development, highlighting their redundant status and indicating that a special challenge exists in wheat gene modification to deal with this high redundancy. However, our results suggested that the hypermorphic effect of T. aestivum GSK (TaGSK) genes with point mutations may be an effective approach to overcome this redundancy in the manipulation of BR signaling in wheat. Our study provides fundamental data uncovering the function of BR in wheat root development, the underlying genetic basis and a possible strategy to manipulate BR signaling in hexaploid wheat.
Identification of Arabidopsis CCR4-NOT Complexes with Pumilio RNA-Binding Proteins, APUM5 and APUM2
Authors: Arae Toshihiro , Morita Kotone , Imahori Riko , Suzuki Yuya , Yasuda Shigetaka , Sato Takeo , Yamaguchi Junji , Chiba Yukako
Published: May 2019

CCR4/CAF1 are widely conserved deadenylases in eukaryotes. They form a large complex that includes NOT1 as a scaffold protein and various NOT proteins that are core components of multiple levels of gene expression control. The CCR4-NOT complex also contains several RNA-binding proteins as accessory proteins, which are required for target recognition by CCR4/CAF1 deadenylases. AtCCR4a/b, orthologs of human CCR4 in Arabidopsis, have various physiological effects. AtCCR4 isoforms are likely to have specific target mRNAs related to each physiological effect; however, AtCCR4 does not have RNA-binding capability. Therefore, identifying factors that interact with AtCCR4a/b is indispensable to understand its function as a regulator of gene expression, as well as the target mRNA recognition mechanism. Here, we identified putative components of the AtCCR4-NOT complex using co-immunoprecipitation in combination with mass spectrometry using FLAG-tagged AtCCR4b and subsequent verification with a yeast two-hybrid assay. Interestingly, four of 11 AtCAF1 isoforms interacted with both AtCCR4b and AtNOT1, whereas two isoforms interacted only with AtNOT1 in yeast two-hybrid assays. These results imply that Arabidopsis has multiple CCR4-NOT complexes with various combinations of deadenylases. We also revealed that the RNA-binding protein Arabidopsis Pumilio 5 and 2 interacted with AtCCR4a/b in the cytoplasm with a few foci.
Essential and Detrimental — an Update on Intracellular Iron Trafficking and Homeostasis
Authors: Vigani Gianpiero , Solti ï¿½dï¿½m , Thomine Sï¿½bastien , Philippar Katrin
Published: May 2019

Chloroplasts, mitochondria and vacuoles represent characteristic organelles of the plant cell, with a predominant function in cellular metabolism. Chloroplasts are the site of photosynthesis and therefore basic and essential for photoautotrophic growth of plants. Mitochondria produce energy during respiration and vacuoles act as internal waste and storage compartments. Moreover, chloroplasts and mitochondria are sites for the biosynthesis of various compounds of primary and secondary metabolism. For photosynthesis and energy generation, the internal membranes of chloroplasts and mitochondria are equipped with electron transport chains. To perform proper electron transfer and several biosynthetic functions, both organelles contain transition metals and here iron is by far the most abundant. Although iron is thus essential for plant growth and development, it becomes toxic when present in excess and/or in its free, ionic form. The harmful effect of the latter is caused by the generation of oxidative stress. As a consequence, iron transport and homeostasis have to be tightly controlled during plant growth and development. In addition to the corresponding transport and homeostasis proteins, the vacuole plays an important role as an intracellular iron storage and release compartment at certain developmental stages. In this review, we will summarize current knowledge on iron transport and homeostasis in chloroplasts, mitochondria and vacuoles. In addition, we aim to integrate the physiological impact of intracellular iron homeostasis on cellular and developmental processes.
Against Contextualism about Prudential Discourse
Authors: Fletcher Guy
Published: May 2019

In recent times, there has been a surge of interest in, and enthusiasm for, contextualist views about prudential discourse—thought and talk about what has prudential value or contributes to someone's well-being. In this paper, I examine and reject two cases for radical forms of prudential contextualism, proposed by Anna Alexandrova and Steve Campbell. Alexandrova holds that the semantic content of terms like ‘well-being’ and ‘doing well’ varies across contexts. Campbell proposes that there are plural prudential concepts at play in prudential discourse (and in philosophical reflection upon such discourse) and that we find evidence of this in the conflicting commitments of prudential discourse. The negative aim of the paper is to show that Alexandrova and Campbell have not given us a good case for ambitious forms of contextualism about prudential discourse. The positive aim of the paper is to provide alternative, aspectualist, explanations of the features of prudential discourse that their discussions highlight.
Rolling back the prison estate: the pervasive impact of macroeconomic austerity on prisoner health in England
Authors: Ismail Nasrul
Published: May 2019

Prisons offer policymakers an opportunity to address the pre-existing high prevalence of physical and mental health issues among prisoners. This notion has been widely integrated into international and national prison health policies, including the Healthy Prisons Agenda, which calls for governments to address the health needs of prisoners and safeguard their health entitlement during imprisonment, and the Sustainable Development Goals 2030 concerning reducing inequality among disadvantaged populations.

However, the implementation of the austerity policy in the United Kingdom since the re-emergence of the global financial crisis in 2008 has impeded this aspiration. This interdisciplinary paper critically evaluates the impact of austerity on prison health. The aforementioned policy has obstructed prisoners’ access to healthcare, exacerbated the degradation of their living conditions, impeded their purposeful activities and subjected them to an increasing level of violence.

This paper calls for alternatives to imprisonment, initiating a more informed economic recovery policy, and relying on transnational and national organizations to scrutinize prisoners’ entitlement to health. These systemic solutions could act as a springboard for political and policy discussions at national and international forums with regard to improving prisoners’ health and simultaneously meeting the aspirations of the Healthy Prisons Agenda and the Sustainable Development Goals.
Cross-Listings and the Dynamics between Credit and Equity Returns
Authors: Augustin Patrick , Jiao Feng , Sarkissian Sergei , Schill Michael J
Published: May 2019

We study how listing in multiple markets affects the dynamics between firms’ credit default swap (CDS) and stock returns. We find that cross-listing increases (1) the sensitivity of CDS to stock returns, (2) the integration of CDS with world equity and bond markets, and (3) the statistical synchronicity of CDS and stock prices. Our results are stronger for firms with greater media attention, analyst and CDS coverage, and Google search intensity and for listings in familiar markets. We suggest that a firm’s presence in global equity markets comes with an improvement in the credit-equity integration through a reduction of informational frictions.

Received April 20, 2017; editorial decision February 12, 2019 by Editor Andrew Karolyi. Authors have furnished an Internet Appendix, which is available on the Oxford University Press Web site next to the link to the final published paper online.
STRESS MANAGEMENT FOR DISASTER RECOVERY SUPPORT STAFF ASSISTING NUCLEAR DISASTER EVACUEES
Authors: Kawazoe I , Kidachi R , Norikane K , Tanaka M , Tanaba S
Published: May 2019

The residents of Town A have been taking shelter in various parts of Japan ever since the accident of Fukushima Daiichi Nuclear Power Plant. The staff members carry out their tasks in seven locations across the country under a great stress with the limited manpower. This study reports the present situation of the stress management for the disaster recovery support staff helping the evacuees living outside the prefecture. The subjects were the 19 members. The T-scores were calculated from Coping Inventory for Stressful Situations (CISS) by assessing their CISS before the mental health seminars commenced. There was a significant positive correlation between ‘task-oriented coping’ and ‘avoidance-oriented coping’ as well as ‘task-oriented coping’ and ‘amusement’. Between the genders, the male subjects expressed a significantly higher ‘amusement’ value.
APPLICABILITY OF AUTONOMOUS UNMANNED HELICOPTER SURVEY OF AIR DOSE RATE IN SUBURBAN AREA
Authors: Yoshimura K , Fujiwara K , Nakama S
Published: May 2019

An autonomous unmanned helicopter (AUH) survey is a useful tool for monitoring the distribution of ambient dose equivalent rates. However, the AUH survey method was developed for plane permeable fields such as agricultural land, and its applicability to urban areas is unclear. In this study, the applicability was investigated by comparing the results of AUH and ground-based surveys conducted in suburban areas, including residential and agricultural lands. The results of both surveys broadly agreed with each other within a factor of 2 in the range independent of land use, and the factor was the same as that reported for plane permeable fields. These results suggest that AUH surveys are applicable in urban areas. The measurement uncertainty of the AUH survey was largely affected by the patchy and local distribution of ambient dose equivalent rates on the ground and differences in the fields of view, rather than land use.
Electrical resistivity tomography: patterns in Betula pendula, Fagus sylvatica, Picea abies and Pinus sylvestris
Authors: Bär Andreas , Hamacher Monika , Ganthaler Andrea , Losso Adriano , Mayr Stefan
Published: May 2019

Electrical resistivity (ER) tomography is a promising technique to minimally invasively study stems of living trees. It allows insights into xylem properties based on the cross-sectional distribution of ER that is governed by the wood’s electrical conductance. In this study, ER measurements were carried out on four forest tree species, Betula pendula, Fagus sylvatica, Picea abies and Pinus sylvestris, to demonstrate interspecific, intraspecific and within-tree variation of ER tomograms. Further, ER patterns were linked to xylem moisture content (MC), electrolyte content and density obtained from wood core analyses. The ER patterns of both coniferous species, P. abies and P. sylvestris, were found to be more homogenous and concentric compared with the complex tomograms of angiosperms. However, the ER range of coniferous trees showed considerable intraspecific variation. Measurements near ground level showed pronounced effects on ER tomograms, highlighting the importance of the chosen measurement height. A strong relation between ER and wood density was found in F. sylvatica while ER patterns of conifers were mainly influenced by MC. Results demonstrate a high species specificity of ER tomograms and of respective influencing xylem traits. They underline the importance of reference measurements for a correct interpretation of ER studies.
Accounting for red blood cell accessibility reveals distinct invasion strategies inPlasmodium falciparumstrains
Authors: Cai Francisco , DeSimone Tiffany M. , Hansen Elsa , Jennings Cameron V. , Bei Amy K. , Ahouidi Ambroise D. , Mboup Souleymane , Duraisingh Manoj T. , Buckee Caroline O.
Published: May 2019

The growth of the malaria parasitePlasmodium falciparumin human blood causes all clinical manifestations of malaria, a process that begins with the invasion of red blood cells. Parasites enter red blood cells using distinct pairs of parasite ligands and host receptors that define particular invasion pathways. Parasite strains have the capacity to switch between invasion pathways. This flexibility is thought to facilitate immune evasion against particular parasite ligands, but may also reflect the fact that red blood cell surfaces are dynamic and composed of heterogeneous invasion targets. Different host genetic backgrounds affecting red blood cell structure have long been recognized to impact parasite growthin vivo, but even within a host, red blood cells undergo dramatic changes in morphology and receptor density as they age. The consequences of these heterogeneities for parasite growthin vivoremain unclear. Here, we measured the ability of laboratory strains ofP. falciparumrelying on distinct invasion pathways to enter red blood cells of different ages. We estimated invasion efficiency while accounting for the fact that even if the red blood cells display the appropriate receptors, not all are physically accessible to invading parasites. This approach revealed a tradeoff made by parasites between the fraction of susceptible cells and their invasion rate into them. We were able to distinguish between “specialist” strains exhibiting high invasion rate in fewer cells versus “generalist” strains invading less efficiently into a larger fraction of cells. We developed a mathematical model to predict that infection with a generalist strain would lead to higher peak parasitemiasin vivowhen compared with a specialist strain with similar overall proliferation rate. Thus, the heterogeneous ecology of red blood cells may play a key role in determining the rate of parasite proliferation between different strains ofP. falciparum.
Using Earth Mover’s Distance for Viral Outbreak Investigations
Authors: Melnyk Andrew , Knyazev Sergey , Vannberg Fredrik , Bunimovich Leonid , Skums Pavel , Zelikovsky Alex
Published: May 2019

RNA viruses mutate at extremely high rates forming an intra-host viral population of closely related variants (or quasi-species) [4]. High variability of Human Immunodeficiency Virus (HIV) and Hepatitis C virus (HCV) making them particularly dangerous by allowing them to evade the host’s immune system. HIV and HCV outbreaks pose a significant problem for public health for solving which it is critical to infer transmission clusters, i.e., to decide whether two viral samples belong to the same outbreak. Initial approach [10] was based on estimating relatedness between two samples as the distance between consensuses of the corresponding viral populations. The distance between closest pair of representatives from two populations, MinDist, has been shown to be significantly more accurate [2]. Unfortunately, MinDist computation requires a cumbersome RNA-seq data assembly and identification of all viral sequences from a given project. We present a novel approach that allows to bypass read assembly and estimate the distance between viral samples based on k-mer (i.e. a substring of length k) distribution in RNA-seq reads. The experimental validation using sequencing data from HCV outbreaks shows that the proposed algorithms can successfully identify genetic relatedness between viral populations, infer transmission clusters and outbreak sources, as well decide whether the primary spreader is present in the sequenced outbreak sample.
Genome rearrangements and megaplasmid loss in the filamentous bacteriumKitasatospora viridifaciensare associated with protoplast formation and regeneration
Authors: Ramijan Karina , Zhang Zheren , van Wezel Gilles P. , Claessen D.
Published: May 2019

Filamentous Actinobacteria are multicellular bacteria with linear replicons.Kitasatospora viridifaciensDSM 40239 contains a linear 7.8 Mb chromosome and an autonomously replicating plasmid KVP1 of 1.7 Mb. Here we show that lysozyme-induced protoplast formation of the multinucleated mycelium ofK. viridifaciensdrives morphological diversity. Characterization and sequencing of an individual revertant colony that had lost the ability to differentiate revealed that the strain had not only lost most of KVP1 but also carried lesions in the right arm of the chromosome. Strikingly, the lesion sites were preceded by insertion sequence elements, suggesting that the rearrangements may have been caused by replicative transposition and homologous recombination between both replicons. These data indicate that protoplast formation is a stressful process that can lead to profound genetic changes.

Repositories

Genomic sequence data for strain B3.1 has been deposited in the NCBI SRA database under accession code SAMN11514356.
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

Many 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.

Synopsis

Suborganelle 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

Prefrontal 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

Cell 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

High 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

Conventional 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

Nuclear 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

Hippocampal 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 STATEMENT

Neuronal 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

Chronic 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.
An enhanced pose tracking method using progressive scan matching
Authors: Yuan Rupeng , Zhang Fuhai , Qu Jiadi , Li Guozhi , Fu Yili
Published: May 2019

Purpose

The purpose of this paper is to propose an enhanced pose tracking method using progressive scan matching, focusing on accuracy, time efficiency and robustness.

Design/methodology/approach

The general purpose of localization algorithms is to dynamically track a robot instead of globally locating one. In this paper, progressive scan matching is used to promote the performance of pose tracking. Rotational and translational samples are separately generated to accelerate the calculation and to increase the accuracy. Progressive iteration of sample generation can ensure localization to achieve a specific precision. The direction of localization uncertainty is taken into consideration to increase robustness. Nonlinear optimization is adopted to achieve a more precise result.

Findings

The proposed method was implemented on a self-made mobile robot. Two experiments were conducted to test the accuracy and time efficiency of the method. The comparison with the basic Monte Carlo localization shows the advantages of the method. Another two experiments were conducted to test the robustness of the method. The result shows that the method can relocate a robot from an inaccurate place if the offset is moderate.

Originality/value

An enhanced pose tracking method is proposed to promote the performance by separately processing rotational and translational samples, progressively iterating the sample generation, taking the direction of localization uncertainty into consideration and adopting nonlinear optimization. The proposed method enables a robot to accurately and quickly locate itself in the environment with robustness.
Evaluating library service quality of University of Kashmir: a LibQUAL+ survey
Authors: Kumar Anil , Mahajan Preeti
Published: May 2019

Purpose

The purpose of this paper is to evaluate the library service quality (LSQ) of University of Kashmir from the users’ perspectives based on the LibQUAL+ model approach.

Design/methodology/approach

The survey used the LibQUAL+ model to evaluate service quality (SQ) of Allama Iqbal Library (AIL), University of Kashmir, Srinagar (India). The data were collected from library users by administering the LibQUAL+ questionnaire in a printed format.

Findings

It has been revealed that AIL has succeeded in satisfying the minimum expectations of its users but could not meet the customers’ desired expectations that make them delighted. Library as Place (LP) and Information Control (IC) are the most satisfied dimensions of SQ of AIL, whereas Affect of Service (AS) is the least satisfied dimension. LP is the most desired dimension amongst LibQUAL+ dimensions. All LibQUAL+ items were found to be lying inside the zone of tolerance (ZoT). Further, “Library is secure and peaceful place for study, learning and research” (LP-21) was found as most important service item as per users’ desired expectations, while “Library staff shows dependability in handling users’ service problems” (AS-9) is marked as the least desired item.

Originality/value

Only a few studies have been carried out to evaluate the SQ of Indian university libraries as far as the LibQUAL+ model is concerned. Therefore, the findings of present survey will help to understand how far library has reached in satisfying users’ expectations as well as the areas or dimensions where it needs to improve.