bluuebunny/crossref_metadata_2025 huggingface dataset:
Microbiomes and Pathogen Survival in Crop Residues, an Ecotone Between Plant and Soil
Authors: Kerdraon Lydie , Laval Valérie , Suffert Frédéric
Published: August 2019

The negative contribution of crop residues as a source of inoculum for plant diseases is well established. However, microbial ecologists have long reported positive effects of residues on the stability of agrosystems and conservation tillage practices have become increasingly widespread. Most studies have suggested that large microbial communities should be taken into account in plant disease management, but we know little about their ecological interaction with pathogens in the crop residue compartment. This review focuses on microbiomes associated with residues within the context of other microbial habitats in cereal-producing agroecosystems such as phyllosphere or rhizosphere. We connected residue microbiome with the survival of residue-borne fungal plant pathogens, thus combining knowledge in microbial ecology and epidemiology, two disciplines still not sufficiently connected. We provide an overview of the impact of residues on cereal disease epidemics and how dynamic interactions between microbial communities of nonburied residues during their degradation, along with soil and multitude of abiotic factors, can contribute to innovative disease management strategies, including next-generation microbiome-based biocontrol strategies. Starting from the classical but still relevant view of crop residues as a source of pathogen inoculum, we first consider possibilities for limiting the amount of residues on the soil surface to reduce the pathogen pressure. We then describe residues as a transient half-plant/half-soil compartment constituting a key fully fledged microbial ecosystem: in other words, an ecotone which deserves special attention. We focus on microbial communities, the changes in these communities over time and the factors influencing them. Finally, we discuss how the interactions between the microbial communities and the pathogens present on residues could be used: identification of keystone taxa and beneficial assemblages, then preservation of these taxa by adapted agronomic practices or development of synthetic communities, rather than the introduction of a single exogenous biocontrol species designed as a treatment product.

[Formula: see text] Copyright © 2019 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
Incidence Rate of Gastric Cancer Adenocarcinoma in Patients With Gastric Dysplasia
Authors: Akbari Maryam , Kardeh Bahareh , Tabrizi Reza , Ahmadizar Fariba , Lankarani Kamran B.
Published: August 2019

Several studies have reported the risk of progression to gastric adenocarcinoma (GAC) in patients with gastric dysplasia (GD); however, the findings are controversial. We performed a systematic review and meta-analysis to study the incidence rate of GAC among patients with GD. Using a comprehensive search strategy, we systematically searched online databases including PubMed, Scopus, EMBASE, Cochrane Library, and Web of Science databases for identifying all relevant original articles through inception until July 2018. Cochran Q and I
2 tests were used to assess heterogeneities between included studies. The incidence rates of GAC and their corresponding 95% confidence intervals (CIs) were pooled using random-effect or fixed-effect models. Of the 1980 retrieved records, 30 eligible articles (61 studies) were included. The overall pooled incidence rate of GAC was 40.36 (95% CI, 27.08-55.71; I
2, 96.0%) cases per 1000 person-years in patients with GD. Subgroup analysis according to the type of GD indicated the highest incidence rate of GAC was 186.40 (95% CI, 106.63-285.60; I
2, 94.6%) per 1000 person-years among patients with high-grade dysplasia (HGD) lesions. Although the incidence rates of GAC in low-grade dysplasia (LGD) lesions and in nonclassified lesions were 11.25 (95% CI, 3.91-21.22; I
2, 89.3%), and 1.40 (95% CI, 0.00-9.71; I
2, 78.8%), respectively. Compared with patients with LGD lesions, progression rate from GD to GAC was roughly 16 times greater in patients with HGD lesions. As the majority of patients with GAC are diagnosed in an advanced stage our study suggests strict management of HGD lesions to prevent GAC.
Clinical Decision Support to Improve Dosing Weight Use in Infants with Neonatal Abstinence Syndrome
Authors: Bertoni C. Briana , Prusakov Pavel , Merandi Jenna , Bartman Thomas
Published: August 2019

Introduction:

Opioid abuse in the United States is a public health emergency. From 2000 to 2009, prenatal maternal opiate use increased from 1.19 to 5.63 per 1,000 births, with up to 80% of in utero opioid-exposed infants requiring pharmacotherapy. This study aimed to increase the percentage of neonatal abstinence syndrome (NAS) medication orders based on birth weight (BW) in neonates admitted to a neonatal intensive care unit with a principal diagnosis of NAS from 29% to 90%, within 4 months of project initiation, and to sustain this for 6 months.

Methods:

This project occurred at an academic medical center with 5,000 deliveries per year and a 49-bed Level III neonatal intensive care unit. We used the Institute for Healthcare Improvement methodology, largely focusing interventions on clinical decision support (CDS) tools. We plotted all measures on Shewhart charts, and Nelson rules differentiated special versus common cause variation.

Results:

The percent of orders based on BW increased from 29% to 78% after implementing multiple interventions focused primarily on CDS. However, this later decreased to 48% as workarounds began. There was also a significant decrease in the length of stay variability, which persisted throughout the project.

Discussion:

CDS is a helpful tool to guide prescribing behavior; however, workarounds can negate its usefulness. Standardized use of BW for weight-based NAS medication prescribing can decrease the length of stay variability. Further studies are needed using a human factors approach to minimize workarounds in CDS and potentially decrease the length of stay in neonates with NAS.
Sir David Cecil Smith. 21 May 1930—29 June 2018
Authors: Douglas Angela E.
Published: August 2019

David Smith was an international authority in the biological discipline of symbiosis and an influential leader in academic life. Through his work on photosynthetic symbioses in lichens and invertebrate animals, David transformed the field of symbiosis from a study of taxonomy and morphology into an experimental science. In particular, he applied novel radiotracer techniques to demonstrate that lichens are metabolically dynamic, with photosynthetically-fixed carbon transferred from symbionts to lichen host at high rates. His subsequent study of diverse symbioses led him to develop common principles underlying symbioses, including the regulated transfer of metabolites between partners and the role of ecological processes of colonization and community assembly in the establishment of symbioses. In his academic service, David had multiple leadership roles, including head of the Department of Botany at University of Bristol (1974–1980), head of the Department of Agricultural Science at University of Oxford (1980–1987), principal of University of Edinburgh (1987–1994) and president of Wolfson College, University of Oxford (1994–2000). David was biological secretary of the Royal Society (1983–1987) and he was knighted in 1986.
James Alexander Green. 26 February 1926—7 April 2014
Authors: Donkin Stephen , Erdmann Karin
Published: August 2019

James Alexander Green, known as Sandy, was a mathematician of great influence and distinction. He was an algebraist, famous for his work on modular representations of finite groups, and the development of the theory of polynomial representations of general linear groups.

He was elected Fellow of the Royal Society of Edinburgh (1968) and Fellow of the Royal Society of London (1987). He was awarded prizes of the London Mathematical Society, a Senior Berwick Prize (in 1984) and the De Morgan Medal (in 2001).

In his doctoral thesis, on semigroups, Sandy introduced fundamental relations, now known as ‘Green's relations’. He determined the characters of arbitrary finite general linear groups published 1955. Sandy then turned to representations of finite groups over fields of prime characteristic; his work laid the foundations for the module theoretic approach to the subject. His next highlight is his monograph on polynomial representations of
GL

n

, published in 1980, which has become the basis for algebraic highest weight theory. Furthermore, in 1995 he proved a fundamental result on Hall algebras, establishing a connection between quantum groups and representations of finite-dimensional quiver algebras.
A coarse-grained model of the expansion of the human rhinovirus 2 capsid reveals insights in genome release
Authors: Indelicato Giuliana , Cermelli Paolo , Twarock Reidun
Published: August 2019

Human rhinoviruses are causative agents of the common cold. In order to release their RNA genome into the host during a viral infection, these small viruses must undergo conformational changes in their capsids, whose detailed mechanism is strictly related to the process of RNA extrusion, which has been only partially elucidated. We study here a mathematical model for the structural transition between the native particle of human rhinovirus type 2 and its expanded form, viewing the process as an energy cascade, i.e. a sequence of metastable states with decreasing energy connected by minimum energy paths. We explore several transition pathways and discuss their implications for the RNA exit process.
Mathematical modelling to study the horizontal transfer of antimicrobial resistance genes in bacteria: current state of the field and recommendations
Authors: Leclerc Quentin J. , Lindsay Jodi A. , Knight Gwenan M.
Published: August 2019

Antimicrobial resistance (AMR) is one of the greatest public health challenges we are currently facing. To develop effective interventions against this, it is essential to understand the processes behind the spread of AMR. These are partly dependent on the dynamics of horizontal transfer of resistance genes between bacteria, which can occur by conjugation (direct contact), transformation (uptake from the environment) or transduction (mediated by bacteriophages). Mathematical modelling is a powerful tool to investigate the dynamics of AMR; however, the extent of its use to study the horizontal transfer of AMR genes is currently unclear. In this systematic review, we searched for mathematical modelling studies that focused on horizontal transfer of AMR genes. We compared their aims and methods using a list of predetermined criteria and used our results to assess the current state of this research field. Of the 43 studies we identified, most focused on the transfer of single genes by conjugation inEscherichia coliin culture and its impact on the bacterial evolutionary dynamics. Our findings highlight the existence of an important research gap in the dynamics of transformation and transduction and the overall public health implications of horizontal transfer of AMR genes. To further develop this field and improve our ability to control AMR, it is essential that we clarify the structural complexity required to study the dynamics of horizontal gene transfer, which will require cooperation between microbiologists and modellers.
Biochemical analysis of nucleosome targeting by Tn5 transposase
Authors: Sato Shoko , Arimura Yasuhiro , Kujirai Tomoya , Harada Akihito , Maehara Kazumitsu , Nogami Jumpei , Ohkawa Yasuyuki , Kurumizaka Hitoshi
Published: August 2019

Tn5 transposase is a bacterial enzyme that integrates a DNA fragment into genomic DNA, and is used as a tool for detecting nucleosome-free regions of genomic DNA in eukaryotes. However, in chromatin, the DNA targeting by Tn5 transposase has remained unclear. In the present study, we reconstituted well-positioned 601 dinucleosomes, in which two nucleosomes are connected with a linker DNA, and studied the DNA integration sites in the dinucleosomes by Tn5 transposase
in vitro
. We found that Tn5 transposase preferentially targets near the entry–exit DNA regions within the nucleosome. Tn5 transposase minimally cleaved the dinucleosome without a linker DNA, indicating that the linker DNA between two nucleosomes is important for the Tn5 transposase activity. In the presence of a 30 base-pair linker DNA, Tn5 transposase targets the middle of the linker DNA, in addition to the entry–exit sites of the nucleosome. Intriguingly, this Tn5-targeting characteristic is conserved in a dinucleosome substrate with a different DNA sequence from the 601 sequence. Therefore, the Tn5-targeting preference in the nucleosomal templates reported here provides important information for the interpretation of Tn5 transposase-based genomics methods, such as ATAC-seq.
Integrins are required for synchronous ommatidial rotation in the
Drosophila
eye linking planar cell polarity signalling to the extracellular matrix
Authors: Thuveson Maria , Gaengel Konstantin , Collu Giovanna M. , Chin Mei-ling , Singh Jaskirat , Mlodzik Marek
Published: August 2019

Integrins mediate the anchorage between cells and their environment, the extracellular matrix (ECM), and form transmembrane links between the ECM and the cytoskeleton, a conserved feature throughout development and morphogenesis of epithelial organs. Here, we demonstrate that integrins and components of the ECM are required during the planar cell polarity (PCP) signalling-regulated cell movement of ommatidial rotation in the
Drosophila
eye. The loss-of-function mutations of integrins or ECM components cause defects in rotation, with mutant clusters rotating asynchronously compared to wild-type clusters. Initially, mutant clusters tend to rotate faster, and at later stages they fail to be synchronous with their neighbours, leading to aberrant rotation angles and resulting in a disorganized ommatidial arrangement in adult eyes. We further demonstrate that integrin localization changes dynamically during the rotation process. Our data suggest that core Frizzled/PCP factors, acting through RhoA and Rho kinase, regulate the function/activity of integrins and that integrins thus contribute to the complex interaction network of PCP signalling, cell adhesion and cytoskeletal elements required for a precise and synchronous 90° rotation movement.
The nature of small molecules adsorbed on defective carbon nanotubes
Authors: Li Danhui , Wang Fengting , Zhang Zhiyuan , Jiang Wanrun , Zhu Yu , Wang Zhigang , Zhang Rui-Qin
Published: August 2019

In this work, we perform a comprehensive theoretical study on adsorption of representative 10-electron molecules H
2
O, CH
4
and NH
3
onto defective single-walled carbon nanotubes. Results of adsorption energy and charge transfer reveal the existence of both chemical adsorption (CA) and physical adsorption (PA). While PA processes are common for all molecules, CA could be further achieved by the polar molecule NH
3
, whose lone-pair electrons makes it easier to be bonded with the defective nanotube. Our systematic work could contribute to the understanding on intermolecular interactions and the design of future molecular detectors.
Extensive sampling reveals the phenology and habitat use of Afrotropical parasitoid wasps (Hymenoptera: Ichneumonidae: Rhyssinae)
Authors: Hopkins Tapani , Roininen Heikki , Sääksjärvi Ilari E.
Published: August 2019

Tropical invertebrates, such as the ichneumonids of tropical forests, are poorly known. Here, we report the first results of extensive sampling at Kibale National Park, Uganda, by providing some of the first tropical ecological data for the ichneumonid subfamily Rhyssinae. We sampled ichneumonids with 34 Malaise traps for a year in 10 sites, in habitats ranging from primary forest to farmland. We also gathered weather and vegetation data. The total sampling effort was 373 trap months and we caught 444 rhyssines in six species. We caught the most rhyssines in dry weather, and towards the end of the sampling year. The rhyssines showed a clear preference for decaying logs and for primary forest. We fitted a model which can be used to predict future catches at the site, and draw conclusions on when rhyssines emerge and on their adult lifespan. Sampling extensively gave us a wealth of ecological data on a poorly known parasitoid wasp subfamily. We recommend that future tropical sampling collect ecological data, and that existing data from previous large-scale surveys be used for ecological analyses.
The environmental predictors of spatio-temporal variation in the breeding phenology of a passerine bird
Authors: Shutt Jack D. , Cabello Irene Benedicto , Keogan Katharine , Leech David I. , Samplonius Jelmer M. , Whittle Lorienne , Burgess Malcolm D. , Phillimore Albert B.
Published: August 2019

Establishing the cues or constraints that influence avian timing of breeding is the key to accurate prediction of future phenology. This study aims to identify the aspects of the environment that predict the timing of two measures of breeding phenology (nest initiation and egg laying date) in an insectivorous woodland passerine, the blue tit (Cyanistes caeruleus). We analyse data collected from a 220 km, 40-site transect over 3 years and consider spring temperatures, tree leafing phenology, invertebrate availability and photoperiod as predictors of breeding phenology. We find that mean night-time temperature in early spring is the strongest predictor of both nest initiation and lay date and suggest this finding is most consistent with temperature acting as a constraint on breeding activity. Birch budburst phenology significantly predicts lay date additionally to temperature, either as a direct cue or indirectly via a correlated variable. We use cross-validation to show that our model accurately predicts lay date in two further years and find that similar variables predict lay date well across the UK national nest record scheme. This work refines our understanding of the principal factors influencing the timing of tit reproductive phenology and suggests that temperature may have both a direct and indirect effect.
Food web structure selects for parasite host range
Authors: Park A. W.
Published: August 2019

Complex life cycle parasites, including helminths, use intermediate hosts for development and definitive hosts for reproduction, with interactions between the two host types governed by food web structure. I study how a parasite's intermediate host range is controlled by the diet breadth of definitive host species and the cost of parasite generalism, a putative fitness cost that assumes host range trades off against fitness derived from a host species. In spite of such costs, a benefit to generalism may occur when the definitive host exhibits a large diet breadth, enhancing transmission of generalist parasites via consumption of a broad array of infected intermediate hosts. I develop a simple theoretical model to demonstrate how different host range infection strategies are differentially selected for across a gradient of definitive host diet breadth according to the cost of generalism. I then use a parasitic helminth–host database in conjunction with a food web database to show that diet breadth of definitive hosts promotes generalist infection strategies at the intermediate host level, indicating relatively low costs of parasite generalism among helminths.
Effect of argon- and nitrogen-based modified atmosphere packaging on shiitake mushroom quality
Authors: Park Jong-Jin , Lee Jae-Jun , Olawuyi Ibukunoluwa Fola , Lee Wonyoung
Published: August 2019

The effect of modified atmosphere packaging (MAP) on shiitake mushroom quality was investigated using different types of gases (air, nitrogen and argon). The mushrooms were placed in a composite polyethylene-polyamide package, and then the package was evacuated, flushed with desired gas, and heat-sealed. The packaged mushrooms were stored at 5 and 15℃ for 21 days. During storage, the color, texture, gas composition, weight loss, microorganism count and polyphenol oxidase (PPO) activity were measured. Carbon dioxide production, weight loss, color change, PPO activity, microorganism count and decline of hardness were more inhibited at 5℃ than at 15℃. The MAP used did not affect the weight loss or microbial count. However, mushroom in the argon (Ar) MAP had the lowest carbon dioxide production followed by those in the nitrogen (N) MAP and then the air filled control packaging (C). At 15℃, the L* value of the mushroom gills in the Ar and N MAP maintained throughout the storage time. Of particular note, mushrooms in Ar MAP retained hardness at 5 and 15℃, unlike those of the control. PPO activity was inhibited by the Ar and N MAP at 15℃. Based on these results, the quality of shiitake mushrooms was best preserved during storage by the Ar MAP.
Quality and antioxidant properties of jelly supplemented with apricot juice concentrate
Authors: Lee Jun Ho , Kim So Yeon
Published: August 2019

Gummy jellies are becoming more popular than in the past as a dessert or snack in the Korean food market. Taking advantages of diverse functional activities of apricot juice concentrate (AJC), it can be incorporated into snack food such as jelly to meet consumers’ emerging demands regarding health concerns. However, there has been a scarcity of reports on the most appropriate concentration of AJC in jellies. This prompted us to undertake the present investigation with the objective to evaluate the physical, sensory, and antioxidant characteristics of jellies containing various concentrations of AJC (7.5%, 15%, 22.5%, and 30%). The pH, moisture content, and lightness (L*) decreased significantly while total soluble solids (TSS), hardness, redness (a*), and yellowness (b*) increased significantly with increasing concentrations AJC (p<0.05). In addition, the 2,2-diphenyl-1-picrylhydrazyl (DPPH) and 2,2’-azino-bis-3-ethylbenzothiazoline-6-sulfonic acid (ABTS) radical scavenging activities significantly increased (p<0.05) at higher AJC concentrations. A consumer acceptance test indicated that the incorporation of 22.5% AJC had favorable effects on consumer preferences for all the tested attributes. Based on our study, jelly incorporated with 22.5% AJC is recommended for developing AJC-supplemented jellies with improved overall qualities without sacrificing consumer acceptability and while taking advantage of the functional properties of AJC.
High-throughput multicolor 3D localization in live cells by depth-encoding imaging flow cytometry
Authors: Weiss Lucien E. , Ezra Yael Shalev , Goldberg Sarah E. , Ferdman Boris , Shechtman Yoav
Published: August 2019

Imaging flow cytometry replaces the canonical point-source detector of flow cytometry with a camera, unveiling subsample details in 2D images while maintaining high-throughput. Here we show that the technique is inherently compatible with 3D localization microscopy by point-spread-function engineering, namely the encoding of emitter depth in the emission pattern captured by a camera. By exploiting the laminar-flow profile in microfluidics, 3D positions can be extracted from cells or other objects of interest by calibrating the depth-dependent response of the imaging system using fluorescent microspheres mixed with the sample buffer. We demonstrate this approach for measuring fluorescently-labeled DNAin vitroand the chromosomal compaction state in large populations of live cells, collecting thousands of samples each minute. Furthermore, our approach is fully compatible with existing commercial apparatus, and can extend the imaging volume of the device, enabling faster flowrates thereby increasing throughput.
Primary complex motor stereotypies are associated with de novo damaging DNA coding mutations that identify candidate risk genes and biological pathways
Authors: Fernandez Thomas V. , Williams Zsanett P. , Kline Tina , Rajendran Shreenath , Augustine Farhan , Wright Nicole , Sullivan Catherine A. W. , Olfson Emily , Abdallah Sarah B. , Liu Wenzhong , Hoffman Ellen J. , Gupta Abha R. , Singer Harvey S.
Published: August 2019

Motor stereotypies are common in children with autism spectrum disorder (ASD), intellectual disability, or sensory deprivation, as well as in typically developing children (“primary” stereotypies, CMS). The precise pathophysiological mechanism for motor stereotypies is unknown, although genetic etiologies have been suggested. In this study, we perform whole-exome DNA sequencing in 129 parent-child trios with CMS and 853 control trios (118 cases and 750 controls after quality control). We report an increased rate of de novo predicted-damaging variants in CMS versus controls, identifyingKDM5Bas a high-confidence risk gene and estimating 184 genes conferring risk. Genes harboring de novo damaging variants in CMS probands show significant overlap with those in Tourette syndrome, ASD candidate genes, and those in ASD probands with high stereotypy scores. Furthermore, exploratory biological pathway and gene ontology analysis highlight histone demethylation, organism development, cell motility, glucocorticoid receptor pathway, and ion channel transport. Continued sequencing of CMS trios will identify more risk genes and allow greater insights into biological mechanisms of stereotypies across diagnostic boundaries.
Density-dependent costs and benefits of male mating success in a wild insect
Authors: Niemelä Petri T. , Tiso Stefano , Dingemanse Niels J.
Published: August 2019

Social environments are important determinant of fitness, particularly when same-sex local densities shape both mating success and survival costs.

We studied how mating success varied across a range of naturally occurring local male densities in wild field cricket males,Gryllus campestris, monitored by using fully automated RFID-surveillance system. We predicted that mating success as a function of local density follow a concave pattern predicted by the Allee-effect theory. As increasing density should reduceper capitapredation and parasitism risk, we predicted that males generally having high mating success in low (versus high) local density live less long. Finally, we predicted that males on average occurred in local densities where their mating success is highest.

Male mating success followed a density-dependent pattern predicted by the Allee-effect theory. Males also differed in the local density where their mating success was highest. This variation explained longevity and total fitness: males with high mating success in low local density lived longer and had higher total mating success. Finally, we found no evidence of males occupying local densities in which their mating success is highest.

Our study suggest that density-dependent plasticity in mating success is under selection: males having high mating success in low density, but low mating success in high density, lived longer and had higher overall mating success. We thus provide novel insights, with unseen detail, about individual differences in density-dependent mating success and, costs and benefits related to variation in mating success in the wild. Finally, our study also highlights that specific statistical approaches are needed to firmly study the costs and benefits associated with the traits that are repeatedly expressed across range of environments.
How do three cytosolic glutamine synthetase isozymes of wheat perform N assimilation and translocation?
Authors: Wei Yihao , Wang Xiaochun , Zhang Zhiyong , Xiong Shuping , Zhang Yiming , Wang Lulu , Meng Xiaodan , Zhang Jie , Ma Xinming
Published: August 2019

To understand how the three cytosolic glutamine synthetase (GS1) isozymes of wheat (Triticum aestivum L., TaGS1) perform nitrogen assimilation and translocation, we studied the kinetic properties of TaGS1 isozymes, the effects of nitrogen on the expression and localization of TaGS1 isozymes with specific antibodies, and the nitrogen metabolism. The results showed TaGS1;1, the dominant TaGS1 isozyme, had a high affinity for substrates, and was widely localized in the mesophyll cells, root pericycle and root tip meristematic zone, suggesting it was the primary isozyme for N assimilation. TaGS1;2, with a high affinity for Glu, was activated by Gln, and was mainly localized in the around vascular tissues, indicating that TaGS1;2 catalyzed Gln synthesis in low Glu concentration, then the Gln returned to activate TaGS1;2, which may lead to the rapid accumulation of Gln around the vascular tissues. TaGS1;3 had low affinity for substrates but the highest Vmax among TaGS1, was mainly localized in the root tip meristematic zone; exogenous NH4+ could promote TaGS1;3 expressing, indicating that TaGS1;3 could rapidly assimilate NH4+ to relieve NH4+ toxicity. In conclusion, TaGS1;1, TaGS1;2 and TaGS1;3 have different role in N assimilation, Gln translocation and relieving ammonium toxicity, respectively, and synergistically perform nitrogen assimilation and translocation.

Highlight

Three cytosolic glutamine synthase isozymes of wheat have different role and synergistically perform nitrogen assimilation and translocation.
Temporal-Spatial Visualization of Endogenous Chromosome Rearrangements in Living Cells
Authors: Wang Haifeng , Nakamura Muneaki , Zhao Dehua , Nguyen Cindy M , Yu Cordelia , Lo Albert , Daley Timothy , Russa Marie La , Liu Yanxia , Qi Lei S
Published: August 2019

Visualizing the real-time dynamics of genome rearrangement in single living cells is core to studying genomics and diagnostics. Here, we report a robust, versatile approach named CRISPRLive-cell fluorescentinsituhybridization (LiveFISH) for multi-locus genome tracking and cytogenetic detection in a broad variety of cell types including primary cells. LiveFISH utilizes an intrinsic stability switch of CRISPR guide RNAs, which enables efficient and accurate detection of chromosomal disorders such as Patau Syndrome in prenatal amniotic fluid cells and allows multi-locus tracking in human T lymphocytes. Using LiveFISH, we are able to detect and track real-time spatiotemporal dynamics of non-homologous endogenous chromosome translocations induced by gene editing. This new approach enables FISH imaging in living primary cells, which can provide useful insights into the spatiotemporal changes of genome organization and rearrangements in normal and diseased primary cells and will enable fast cytogenetic visualization of various gene-editing associated chromosomal translocations.
The NAD+-dependent deacetylase Sir2 enables evolution of new traits by regulating distinct gene sets in two yeast species,Saccharomyces cerevisiaeandKluyveromyces lactis
Authors: Humphrey Kristen M. , Zhu Lisha , Hickman Meleah A. , Hasan Shirin , Maria Haniam , Liu Tao , Rusche Laura N.
Published: August 2019

Evolutionary adaptation increases the fitness of an organism in its environment. It can occur through rewiring of gene regulatory networks, such that an organism responds appropriately to environmental changes. We investigated whether sirtuin deacetylases, which repress transcription and require NAD+for activity, could facilitate the evolution of potentially adaptive responses by serving as transcriptional rewiring points. If so, bringing genes under the control of sirtuins could enable organisms to mount appropriate responses to stresses that decrease NAD+levels. To explore how the genomic targets of sirtuins shift over evolutionary time, we compared two yeast species,Saccharomyces cerevisiaeandKluyveromyces lactisthat display differences in cellular metabolism and lifecycle timing in response to nutrient availability. We identified sirtuin-regulated genes through a combination of chromatin immunoprecipitation and RNA expression. In both species, regulated genes were associated with NAD+homeostasis, mating, and sporulation, but the specific genes differed. In addition, regulated genes inK. lactiswere associated with other processes, including utilization of non-glucose carbon sources, heavy metal efflux, DNA synthesis, and production of the siderophore pulcherrimin. Consistent with the species-restricted regulation of these genes, sirtuin deletion impacted relevant phenotypes inK. lactisbut notS. cerevisiae. Finally, sirtuin-regulated gene sets were depleted for broadly-conserved genes, consistent with sirtuins regulating processes restricted to a few species. Taken together, these results are consistent with the notion that sirtuins serve as rewiring points that allow species to evolve distinct responses to low NAD+stress.
Superfast periodicities in distress vocalizations emitted by bats
Authors: Hechavarría Julio C. , Beetz M. Jerome , Garcia-Rosales Francisco , Kössl Manfred
Published: August 2019

Communication sounds are ubiquitous in the animal kingdom, where they play a role in advertising physiological states and/or socio-contextual scenarios. Distress sounds, for example, are typically uttered in distressful scenarios such as agonistic interactions. Here, we report on the occurrence of superfast temporal periodicities in distress calls emitted by bats (speciesCarollia perspicillata). Distress vocalizations uttered by this bat species are temporally modulated at frequencies close to 1.7 kHz, that is, ∼17 times faster than modulation rates observed in human screams. Fast temporal periodicities are represented in the bats’ brain by means of frequency following responses, and temporally periodic sounds are more effective in boosting the heart rate of awake bats than their demodulated versions. Altogether, our data suggest that bats, an animal group classically regarded as ultrasonic, can exploit the low frequency portion of the soundscape during distress calling to create spectro-temporally complex, arousing sounds.
Characterization of the mycobiome of the seagrass,Zostera marina, reveals putative associations with marine chytrids
Authors: Ettinger Cassandra L. , Eisen Jonathan A.
Published: August 2019

Seagrasses are globally distributed marine flowering plants that are foundation species in coastal ecosystems. Seagrass beds play essential roles as habitats and hatcheries, in nutrient cycling and in protecting the coastline from erosion. Although many studies have focused on seagrass ecology, only a limited number have investigated their associated fungi. In terrestrial systems, fungi can have beneficial and detrimental effects on plant fitness. However, not much is known about marine fungi and even less is known about seagrass associated fungi. Here we used culture-independent sequencing of the ribosomal internal transcribed spacer (ITS) region to characterize the taxonomic diversity of fungi associated with the seagrass,Zostera marina. We sampled from twoZ. marinabeds in Bodega Bay over three time points to investigate fungal diversity within and between plants. Our results indicate that there are many fungal taxa for which a taxonomic assignment cannot be made living on and insideZ. marinaleaves, roots and rhizomes and that these plant tissues harbor distinct fungal communities. The most prevalent ITS amplicon sequence variant (ASV) associated withZ. marinaleaves was classified as fungal, but could not initially be assigned to a fungal phylum. We then used PCR with a primer targeting unique regions of the ITS2 region of this ASV and an existing primer for the fungal 28S rRNA gene to amplify part of the 28S rRNA gene region and link it to this ASV. Sequencing and phylogenetic analysis of the resulting partial 28S rRNA gene revealed that the organism that this ASV comes from is a member of Novel Clade SW-I in the order Lobulomycetales in the phylum Chytridiomycota. This clade includes known parasites of freshwater diatoms and algae and it is possible this chytrid is directly infectingZ. marinaleaf tissues. This work highlights a need for further studies focusing on marine fungi and the potential importance of these understudied communities to the larger seagrass ecosystem.
Exploring repost features of police-generated microblogs through topic and sentiment analysis
Authors: Tang XiaoBo , Li Shixuan , Gu Na , Tan MingLiang
Published: August 2019

Purpose

This study aims to explore the repost features of microblogs acting to promote the information diffusion of government-generated content on social media.

Design/methodology/approach

This study proposes a topic−sentiment analysis using a mixed social media analytics framework to analyse the microblogs collected from the Sina Weibo accounts of 30 Chinese provincial police departments. On the basis of this analysis, this study presents the distribution of reposted microblogs and reveals the reposting characteristics of police-generated microblogs (PGMs).

Findings

The experimental results indicate that children’s safety and crime-related PGMs with a positive sentiment can achieve a high level of online information diffusion.

Originality/value

This study is novel, as it reveals the reposting features of PGMs from both a topic and sentiment perspectives, and provides new findings that can inspire users’ reposting behaviour.
Heat transfer analysis on dimple geometries and arrangements in dimple jacketed heat exchanger
Authors: Qian Jin-yuan , Wu Zan , Zhang Qian-Kun , Jin Zhi-Jiang , Sunden Bengt Ake
Published: August 2019

Purpose

The purpose of this paper is to study the effects of dimple geometries and arrangements on the heat transfer enhancement in a dimple jacketed heat exchanger.

Design/methodology/approach

For the purpose of this paper, with the experimental validated numerical model, this paper carries out numerical simulations of both single dimples with different geometries and the whole dimple jacketed heat exchanger with different dimple arrangements. For a single dimple, its secondary vortex flow, temperature differences and the pressure drop performance for different geometries are analyzed. For the whole dimple jacketed heat exchanger, the heat transfer and pressure drop performances are investigated by comparing the no dimple, triangular and rectangular dimple arrangements.

Findings

Results show that dimples can improve the heat transfer efficiency compared with conventional jacketed heat exchanger, and specific geometries and arrangement of dimples for better heat transfer performance are figured out.

Originality/value

This paper considers both dimple geometries and arrangements, which can be useful for further applications in specific integrated devices or similar applications.
Quality improvement in hospice settings: perceptions of leaders
Authors: Singh Jitendra , Sillerud Brandi , Omar Marah
Published: August 2019

Purpose

The purpose of this paper is to explore and examine attitudes and perceptions of leaders on application of quality improvement (QI) strategies in a palliative and hospice care organization.

Design/methodology/approach

This study employed qualitative research methodology where leaders working in a hospice and palliative care organization were invited to participate in 45–60-min-long semi-structured interview. Interviews were recorded and transcribed verbatim. Qualitative content analysis was utilized to analyze the data collected during participant interviews.

Findings

Seven leaders participated in the interviews. Five themes were developed from data analysis: patient-centered care; continuous QI; leadership involvement and commitment; communication as a foundation for QI; and perceived barriers. Data analysis suggests that use of QI approach in palliative and hospice care enhances the quality of care provided for patients, and can help improve patient satisfaction.

Practical implications

Because there is a paucity of research on implementation of QI strategies in hospice and palliative care settings, this research can have wide practical implications. This research can provide useful practical tips to leaders as they work on implementing QI projects in their organization.

Originality/value

This manuscript can be of value to leaders, administrators and academicians who are interested in applying QI principles to healthcare processes especially in palliative and hospice care settings. Ability to work with others, solid communication and involvement of employees from all levels can help in streamlining current systems of care.
Safety attitudes in hospital emergency departments: a systematic review
Authors: Alzahrani Naif , Jones Russell , Rizwan Amir , Abdel-Latif Mohamed E.
Published: August 2019

Purpose

The purpose of this paper is to perform and report a systematic review of published research on patient safety attitudes of health staff employed in hospital emergency departments (EDs).

Design/methodology/approach

An electronic search was conducted of PsychINFO, ProQuest, MEDLINE, EMBASE, PubMed and CINAHL databases. The review included all studies that focussed on the safety attitudes of professional hospital staff employed in EDs.

Findings

Overall, the review revealed that the safety attitudes of ED health staff are generally low, especially on teamwork and management support and among nurses when compared to doctors. Conversely, two intervention studies showed the effectiveness of team building interventions on improving the safety attitudes of health staff employed in EDs.

Research limitations/implications

Six studies met the inclusion criteria, however, most of the studies demonstrated low to moderate methodological quality.

Originality/value

Teamwork, communication and management support are central to positive safety attitudes. Teamwork training can improve safety attitudes. Given that EDs are the “front-line” of hospital care and patients within EDs are especially vulnerable to medical errors, future research should focus on the safety attitudes of medical staff employed in EDs and its relationship to medical errors.
Do the servicescape of public and private hospitals differ? The Malaysian context
Authors: Lai Kim Piew , Chong Siong Choy
Published: August 2019

Purpose

This study aims to explore if public and private hospitals have differing servicescape attributes.

Design/methodology/approach

The study uses a two-stage (EFA and CFA) procedure for identifying the servicescape attributes and examining their validity in the context of public and private hospitals.

Findings

The findings indicate that, in different contexts, patients would expect different aesthetics of servicescape attributes and how they are influenced by the hospital premises.

Research limitations/implications

It is interesting to note that: not all of the attributes that appear in both contexts are exactly the same; patients do not seem to face difficulties in analysing and interpreting directional cues, even though the spatial orientation in private hospitals is relatively smaller; the way patients of public hospitals draw inference about the ambient conditions is not consistent with private hospitals; and patients perceive that private hospitals pay special attention to developing a built environment that facilitates treatment and recovery process via interior layout, as well as decoration and architecture attributes.

Practical implications

The study grounds the servicescape attributes and provides insights to effectively promote public and private hospitals.

Originality/value

This study may be amongst the first to offer servicescape evidence in both the public and private hospitals.
Dog-assisted intervention at a Spanish university: pilot study
Authors: Peña Gil Diana , García García Mercedes , Camilli Trujillo Celia
Published: August 2019

Purpose

Dog-assisted interventions (DAIs) are conducted by universities around the world as innovative methods that improve students’ quality of life. The purpose of this paper is to assess the DAI program’s effect on the stress levels, well-being and social skills of first-year students from different degree programs at Complutense University of Madrid (UCM).

Design/methodology/approach

The study was conducted with 64 first-year students (M=19.20, SD=1.57). The intervention consisted of three weekly sessions of 1-h duration interacting with a therapy dog. The investigation followed a quasi-experimental pre-test/post-test design with measures of attitudes toward DAI, perceived stress, well-being and social skills.

Findings

The results indicated significant improvements in all studied variables.

Research limitations/implications

This study presents some limitations. In the design, the authors lack a control group. Another limitation is related to the sample, which was small. The authors also acknowledge that only one measure of each outcome variable was administered. Likewise, during the interventions, external observations should be added that generate qualitative records focused on student–dog interactions. In addition, physiological measures of stress, such as cortisol levels, should be included in the analysis to further support the obtained results. Nevertheless, as this was a pilot study, future investigations should aim to create a program using a larger sample of both participants as well as and dogs, with a linear/longitudinal design to measure both the mid- and long-term effects.

Practical implications

In addition, this pilot study was implemented to assist in the validation and adjustment of the DAI program for UCM students.

Social implications

By using a DAI program, college students have had the opportunity to reduce their stress and develop their social skills, as well as improve their quality of life as individuals and students. Although the implementation of Compludog was small, it was also promising as a pedagogical practice at UCM.

Originality/value

It was applied for the first time in a Spanish university and provided access to therapy dogs within this context.
Chronicles of one woman’s journey towards well-being: re-membering
Authors: Mullen Jo
Published: August 2019

Purpose

The purpose of this paper is to share the experiences and reflections of one woman’s journey toward well-being.

Design/methodology/approach

A narrative approach has been taken to structure reflections based on lived experience.

Findings

Reflections are offered based on a personal journey toward well-being.

Originality/value

This paper adds to the accounts of the lived experience of the journey toward well-being, and as such, contributes to the understanding of the process of rebuilding a life.
Effect ofAjuga ivaon enzymes involved in the metabolism of cholesterol, in rat fed a cholesterol-enriched diet
Authors: Bouderbala Sherazede , Bouchenak Malika
Published: August 2019

Purpose

This study aims to investigate the effect ofAjuga iva(Ai) on enzymes involved in the metabolism of cholesterol, in rat fed a cholesterol-enriched diet.

Design/methodology/approach

Male Wistar rats (n = 12), weighing 120 ± 5 g were fed on 1 per cent cholesterol-enriched diet [hypercholesterolemic (HC)] for 15 days (d15). After this adaptation phase, HC rats (total cholesterol = 6.5 ± 0.6 mmol/L) were divided into two groups fed the same diet and treated (Ai-HC) or not with (HC) withAifor d15.

Findings

At day 15, inAi-HC group compared to HC, serum triacylglycerol (TG) values were 1.4-fold lower (p = 0.002), whereas unesterified cholesterol (UC) contents were 1.8-fold higher (p = 0.0001). Serum phospholipids (PL) and cholesteryl esters (CE) contents and liver TG, UC, PL and CE values were not sensitive toAi. TC/HDL-C and LDL-HDL1-C/HDL-C ratios were, respectively, 1.8- and 4-fold lower (p = 0.006 andp = 0.04). HDL2-C and HDL3-C amounts were enhanced by 40 and 74 per cent, respectively (p = 0.003 andp = 0.0001). HDL3-UC was 1.6-fold higher (p = 0.006); whereas PL contents were 1.4-fold lower (p = 0.003). HDL3-apo and HDL2-CE contents were similar between groups. A decreased of hydroxy-methyl-glutaryl-coenzyme A reductase and cholesterol 7α-hydroxylase activities (−44 and −25 per cent;p = 0.003 andp = 0.02, respectively) were noted. Lecithin: cholesterol acyltransferase activity was 1.5-fold higher (p = 0.001).

Originality/value

In HC rat,Aiis able to induce hypotriglyceridemia. However, it turns out thatAimay reduce cardiovascular risk by decreasing the reports of atherogenicity and modifying the activities of enzymes involved in the cholesterol metabolism.