bluuebunny/crossref_metadata_2025_split huggingface dataset:
A 3′-end structure in RNA2 of a crinivirus is essential for viral RNA synthesis and contributes to replication-associated translation activity
Authors: Mongkolsiriwattana Chawin , Zhou Jaclyn S. , Ng James C. K. 
Published: October 2016

AbstractThe terminal ends in the genome of RNA viruses contain features that regulate viral replication and/or translation. We have identified a Y-shaped structure (YSS) in the 3′ terminal regions of the bipartite genome of Lettuce chlorosis virus (LCV), a member in the genus Crinivirus (family Closteroviridae). The YSS is the first in this family of viruses to be determined using Selective 2′-Hydroxyl Acylation Analyzed by Primer Extension (SHAPE). Using luciferase constructs/replicons, in vivo and in vitro assays showed that the 5′ and YSS-containing 3′ terminal regions of LCV RNA1 supported translation activity. In contrast, similar regions from LCV RNA2, including those upstream of the YSS, did not. LCV RNA2 mutants with nucleotide deletions or replacements that affected the YSS were replication deficient. In addition, the YSS of LCV RNA1 and RNA2 were interchangeable without affecting viral RNA synthesis. Translation and significant replication were observed for specific LCV RNA2 replicons only in the presence of LCV RNA1, but both processes were impaired when the YSS and/or its upstream region were incomplete or altered. These results are evidence that the YSS is essential to the viral replication machinery and contributes to replication enhancement and replication-associated translation activity in the RNA2 replicons.
RAB39B gene mutations are not linked to familial Parkinson’s disease in China
Authors: Kang Ji-feng , Luo Yang , Tang Bei-sha , Wan Chang-min , Yang Yang , Li Kai , Liu Zhen-hua , Sun Qi-ying , Xu Qian , Yan Xin-xiang , Guo Ji-feng 
Published: October 2016

AbstractRecently, RAB39B mutations were reported to be a causative factor in patients with Parkinson’s disease (PD). To validate the role of RAB39B in familial PD, a total of 195 subjects consisting of 108 PD families with autosomal-dominant (AD) inheritance and 87 PD families with autosomal-recessive (AR) inheritance in the Chinese Han population from mainland China were included in this study. We did not identify any variants in the coding region or the exon-intron boundaries of the gene by Sanger sequencing method in the DNA samples of 180 patients (100 with AD and 80 with AR). Furthermore, we did not find any variants in the RAB39B gene when Whole-exome sequencing (WES) was applied to DNA samples from 15 patients (8 with AD and 7 with AR) for further genetic analysis. Additionally, when quantitative real-time PCR was used to exclude large rearrangement variants in these patients, we found no dosage mutations in RAB39B gene. Our results suggest that RAB39B mutation is very rare in familial PD and may not be a major cause of familial PD in the Chinese Han Population.
CRISPR/Cas9 Targets Chicken Embryonic Somatic Cells In Vitro and In Vivo and generates Phenotypic Abnormalities
Authors: Abu-Bonsrah Kwaku Dad , Zhang Dongcheng , Newgreen Donald F. 
Published: October 2016

AbstractChickens are an invaluable model for studying human diseases, physiology and especially development, but have lagged in genetic applications. With the advent of Programmable Engineered Nucleases, genetic manipulation has become efficient, specific and rapid. Here, we show that the CRISPR/Cas9 system can precisely edit the chicken genome. We generated HIRA, TYRP1, DICER, MBD3, EZH2 and 6 other gene knockouts in two chicken cell lines using the CRISPR/Cas9 system, with no off-target effects detected. We also showed that very large deletions (>75 kb) could be achieved. We also achieved targeted modification by homology-directed repair (HDR), producing MEN2A and MEN2B mutations of the RET gene. We also targeted DGCR8 in neural cells of the chicken embryo by in vivo electroporation. After FACS isolation of transfected cells, we observed appropriate sequence changes in DGCR8. Wholemount and frozen section antibody labelling showed reduction of DGCR8 levels in transfected cells. In addition, there was reduced expression levels of DGCR8-associated genes DROSHA, YPEL1 and NGN2. We also observed morphological differences in neural tissue and cardiac-related tissues of transfected embryos. These findings demonstrate that precisely targeted genetic manipulation of the genome using the CRISPR/Cas9 system can be extended to the highly adaptable in vivo chicken embryo model.
Neural Correlates of Deficits in Humor Appreciation in Gelotophobics
Authors: Chan Yu-Chen 
Published: October 2016

AbstractGelotophobics have social deficits in the form of relative humorlessness and heightened sensitivity to aggressive humor; however, little is known about the neural reward mechanisms for this group. The present study attempted to identify the neural substrates of responses to hostile and non-hostile jokes in gelotophobics and non-gelotophobics. Gelotophobics showed greater activation than did non-gelotophobics in the dorsal corticostriatal system, which comprises the dorsolateral prefrontal cortex and dorsal striatum, suggesting a higher degree of voluntary top-down cognitive control of emotion. As expected, gelotophobics showed less activation in the ventral mesocorticolimbic system (MCL) in response to both hostile and non-hostile jokes, suggesting a relative deficit in the reward system. Conversely, non-gelotophobics displayed greater activation than gelotophobics did in the MCL system, particularly for non-hostile jokes, which suggests a more robust bottom-up emotional response. In response to non-hostile jokes, non-gelotophobics showed greater activation in the ventral MCL reward system, which comprises the midbrain, amygdalae, nucleus accumbens, ventral anterior cingulate cortex, and insula. Psychophysiological interaction analyses further showed that gelotophobics exhibited diminished MCL activation in response to hostile jokes. These group differences may have important implications for our understanding of the neural correlates of social motivation and humor appreciation.
A role for the asexual spores in infection of Fraxinus excelsior by the ash-dieback fungus Hymenoscyphus fraxineus
Authors: Fones Helen Nicola , Mardon Charlotte , Gurr Sarah Jane 
Published: October 2016

AbstractThe invasive pathogen, ash dieback fungusHymenoscyphus fraxineus, is spreading rapidly across Europe. It shows high levels of outcrossing and limited population structure, even at the epidemic front. The anamorphic (asexual) form produces prolific conidia, thought to function solely as spermatia (male gametes), facilitating gene flow between sympatric strains. Here, we show that conidia are capable of germination on ash leaves andin vitro, and can infect seedlingsvialeaves or soil. In leaves, germlings form structures resembling fruiting bodies. Additionally,H. fraxineuscolonises ash debris and grows in soil in the absence of ash tissues. We propose an amended life-cycle in which wind-dispersed, insect-vectored or water-spread conidia infect ash and may sporulatein planta,as well as in forest debris. This amplifies inoculum levels of different strains in ash stands. In combination with their function as spermatia, conidia thus act to maximise gene flow between sympatric strains, including those originally present at low inoculum. Such mixing increases evolutionary potential, as well as enhancing the likelihood of gene introgression from closely-related strains or assimilation of further genetic diversity from parental Asian populations. This scenario increases the adaptability ofH. fraxineusto new climates and, indeed, onto new host species.
Antidepressant indatraline induces autophagy and inhibits restenosis via suppression of mTOR/S6 kinase signaling pathway
Authors: Cho Yoon Sun , Yen Chih-na , Shim Joong Sup , Kang Dong Hoon , Kang Sang Won , Liu Jun O. , Kwon Ho Jeong 
Published: October 2016

AbstractIndatraline is an antidepressive agent and a non-selective monoamine transporter inhibitor that blocks the reuptake of neurotransmitters (dopamine, serotonin, and norepinephrine). In this study, we report that indatraline induces autophagy via the suppression of mTOR/S6 kinase signaling. Autophagy induction was examined by a cell-based high content screening system using LysoTracker, which was followed by monodansylcadaverine staining and transmission electron microscope observation. Indatraline increased the number of EGFP-LC3 cells expressing autophagosomes in the cytoplasm. Conversion of LC3 was further validated by immunoblotting. Indatraline induced autophagy by affecting the AMPK/mTOR/S6K signaling axis and had no influence on the PI3K/AKT/ERK signaling. Moreover, indatraline induced autophagy in smooth muscle cells (SMCs); further, it exhibited therapeutic potential for restenosis by inhibiting SMC accumulation in a rat restenosis model. These results provide new insights into the role of monoamine transporters in autophagy regulation and identify indatraline as a novel agent for inducing autophagy.
Electrosprayed Multi-Core Alginate Microcapsules as Novel Self-Healing Containers
Authors: Hia Iee Lee , Pasbakhsh Pooria , Chan Eng-Seng , Chai Siang-Piao 
Published: October 2016

AbstractAlginate microcapsules containing epoxy resin were developed through electrospraying method and embedded into epoxy matrix to produce a capsule-based self-healing composite system. These formaldehyde free alginate/epoxy microcapsules were characterized via light microscope, field emission scanning electron microscope, fourier transform infrared spectroscopy and thermogravimetric analysis. Results showed that epoxy resin was successfully encapsulated within alginate matrix to form porous (multi-core) microcapsules with pore size ranged from 5–100 μm. The microcapsules had an average size of 320 ± 20 μm with decomposition temperature at 220 °C. The loading capacity of these capsules was estimated to be 79%. Under in situ healing test, impact specimens showed healing efficiency as high as 86% and the ability to heal up to 3 times due to the multi-core capsule structure and the high impact energy test that triggered the released of epoxy especially in the second and third healings. TDCB specimens showed one-time healing only with the highest healing efficiency of 76%. The single healing event was attributed by the constant crack propagation rate of TDCB fracture test. For the first time, a cost effective, environmentally benign and sustainable capsule-based self-healing system with multiple healing capabilities and high healing performance was developed.
Proper motion survey and kinematic analysis of the ρ Ophiuchi embedded cluster
Authors: Ducourant C. , Teixeira R. , Krone-Martins A. , Bontemps S. , Despois D. , Galli P. A. B. , Bouy H. , Le Campion J. F. , Rapaport M. , Cuillandre J. C. 
Published: October 2016

Context. The ρ Ophiuchi molecular complex and in particular the Lynds L1688 dark cloud is unique in its proximity (~130 pc), in its richness in young stars and protostars, and in its youth (0.5 Myr). It is certainly one of the best targets currently accessible from the ground to study the early phases of star-formation. Proper motion analysis is a very efficient tool for separating members of clusters from field stars, but very few proper motions are available in the ρ Ophiuchi region since most of the young sources are deeply embedded in dust and gas.
Aims. We aim at performing a kinematic census of young stellar objects (YSOs) in the ρ Ophiuchi F core and partially in the E core of the L1688 dark cloud.
Methods. We run a proper motion program at the ESO New Technology Telescope (NTT) with the Son of ISAAC (SOFI) instrument over nine years in the near-infrared. We complemented these observations with various public image databases to enlarge the time base of observations and the field of investigation to 0.5° × 0.5°. We derived positions and proper motions for 2213 objects. From these, 607 proper motions were derived from SOFI observations with a ~1.8 mas/yr accuracy while the remaining objects were measured only from auxiliary data with a mean precision of about ~3 mas/yr.
Results. We performed a kinematic analysis of the most accurate proper motions derived in this work, which allowed us to separate cluster members from field stars and to derive the mean properties of the cluster. From the kinematic analysis we derived a list of 68 members and 14 candidate members, comprising 26 new objects with a high membership probability. These new members are generally fainter than the known ones. We measured a mean proper motion of (μαcosδ, μδ) = (−8.2,−24.3) ± 0.8 mas/yr for the L1688 dark cloud. A supervised classification was applied to photometric data of members to allocate a spectral energy distribution (SED) classification to the unclassified members.
Conclusions. We kinematically confirmed that the 56 members that were known from previous studies of the ρ Ophiuchi F cluster and that were also part of our survey are members of the cluster, and we added 26 new members. We defined the evolutionary status of the unclassified members of the cluster. We showed that a large part (23) of these new members are probably brown dwarfs, which multiplies the number of known substellar objects in the cluster by a factor of 3.3.
Assessing change in perceived community leadership readiness in the Obesity Prevention and Lifestyle program
Authors: Kostadinov Iordan , Daniel Mark , Jones Michelle , Cargo Margaret 
Published: October 2016

Issue addressedThe context of community‐based childhood obesity prevention programs can influence the effects of these intervention programs. Leadership readiness for community mobilisation for childhood obesity prevention is one such contextual factor. This study assessed perceived community leadership readiness (PCLR) at two time points in a state‐wide, multisite community‐based childhood obesity prevention program.MethodsPCLR was assessed across 168 suburbs of 20 intervention communities participating in South Australia's Obesity Prevention and Lifestyle (OPAL) program. Using a validated online PCLR tool, four key respondents from each community rated each suburb within their respective community on a nine‐point scale for baseline and 2015. Average PCLR and change scores were calculated using the general linear model with suburbs nested in communities. Relationships between demographic variables and change in PCLR were evaluated using multiple regression. Ease of survey use was also assessed.ResultsAverage PCLR increased between baseline (3.51, s.d. = 0.82) and 2015 (5.23, s.d. = 0.89). PCLR rose in 18 of 20 intervention communities. PCLR was inversely associated with suburb population size (r2 = 0.03, P = 0.03, b = −0.25) and positively associated with intervention duration (r2 change = 0.08, P = 0.00, b = 0.29). Only 8% of survey respondents considered the online assessment tool difficult to use.ConclusionsPCLR increased over the course of the OPAL intervention. PCLR varied between and within communities. Online assessment of PCLR has utility for multisite program evaluations.So what?Use of a novel, resource‐efficient online tool to measure the key contextual factors of PCLR has enabled a better understanding of the success and generalisability of the OPAL program.
Improving the translation of health promotion interventions using effectiveness–implementation hybrid designs in program evaluations
Authors: Wolfenden Luke , Williams Christopher M. , Wiggers John , Nathan Nicole , Yoong Sze Lin 
Published: October 2016

Bridging the gap between research‐based evidence and public health policy and practice is a considerable challenge to public health improvement this century, requiring a rethinking of conventional approaches to health research production and use. Traditionally the process of research translation has been viewed as linear and unidirectional, from epidemiological research to identify health problems and determinants, to efficacy and effectiveness trials and studies of strategies to maximise the implementation and dissemination of evidence‐based interventions in practice. A criticism of this approach is the considerable time it takes to achieve translation of health research into practice. Hybrid evaluation designs provide one means of accelerating the research translation process by simultaneously collecting information regarding intervention impacts and implementation and dissemination strategy. However, few health promotion research trials employ such designs and often fail to report information to enable assessment of the feasibility and potential impact of implementation and dissemination strategies. In addition to intervention effects, policy makers and practitioners also want to know the impact of implementation strategies. This commentary will define the three categories of effectiveness‐implementation hybrid designs, describe their application in health promotion evaluation, and discuss the potential implications of more systematic use of such designs for the translation of health promotion and evaluation.So what?Greater use of effectiveness‐implementation hybrid designs may accelerate research translation by providing more practice‐ and policy‐relevant information to end‐users, more quickly.
High production of a class III lantipeptide AmfS in Streptomyces griseus
Authors: Takano Hideaki , Matsui Yuhei , Nomura Junpei , Fujimoto Masahiro , Katsumata Naoto , Koyama Takafumi , Mizuno Isamu , Amano Shoichi , Shiratori-Takano Hatsumi , Komatsu Mamoru , Ikeda Haruo , Ueda Kenji 
Published: October 2016

Abstract
AmfS, a class III lantipeptide serves as a morphogen in Streptomyces griseus. Here, we constructed a high production system of AmfS in S. griseus. We isolated S. griseus Grd1 strain defective in glucose repression of aerial mycelium formation and found it suitable for the overproduction of AmfS. Two expression vectors carrying the strong and constitutive ermE2 promoter were constructed using a multicopy number plasmid, pIJ702. The use of the Grd1 strain combined with the expression vectors enabled high production of AmfS by S. griseus into its culture broth. The expression system was also effective for the generation of abundant AmfS derived from Streptomyces avermitilis. In addition, site-directed mutagenesis revealed the amino acid residues essential for the morphogen activity of AmfS. These results indicate that the constructed system enables efficient production of class III lantipeptides by Streptomyces.
The (oxalato)aluminate complex as an antimicrobial substance protecting the “shiro” of Tricholoma matsutake from soil micro-organisms
Authors: Nishino Katsutoshi , Shiro Misao , Okura Ryuki , Oizumi Kazuya , Fujita Toru , Sasamori Takahiro , Tokitoh Norihiro , Yamada Akiyoshi , Tanaka Chihiro , Yamaguchi Muneyoshi , Hiradate Syuntaro , Hirai Nobuhiro 
Published: October 2016

Abstract
Tricholoma matsutake, a basidiomycete, forms ectomycorrhizas with Pinus densiflora as the host tree. Its fruiting body, “matsutake” in Japanese, is an edible and highly prized mushroom, and it grows in a circle called a fairy ring. Beneath the fairy ring of T. matsutake, a whitish mycelium-soil aggregated zone, called “shiro” in Japanese, develops. The front of the shiro, an active mycorrhizal zone, functions to gather nutrients from the soil and roots to nourish the fairy ring. Bacteria and sporulating fungi decrease from the shiro front, whereas they increase inside and outside the shiro front. Ohara demonstrated that the shiro front exhibited antimicrobial activity, but the antimicrobial substance has remained unidentified for 50 years. We have identified the antimicrobial substance as the (oxalato)aluminate complex, known as a reaction product of oxalic acid and aluminum phosphate to release soluble phosphorus. The complex protects the shiro from micro-organisms, and contributes to its development.
A Cytoscape app for motif enumeration with ISMAGS
Authors: Van Parys Thomas , Melckenbeeck Ine , Houbraken Maarten , Audenaert Pieter , Colle Didier , Pickavet Mario , Demeester Piet , Van de Peer Yves 
Published: October 2016

Abstract

Summary
We present a Cytoscape app for the ISMAGS algorithm, which can enumerate all instances of a motif in a graph, making optimal use of the motif’s symmetries to make the search more efficient. The Cytoscape app provides a handy interface for this algorithm, which allows more efficient network analysis.

Availability and Implementation
The Cytoscape app for ISMAGS can be freely downloaded from the Cytoscape App store http://apps.cytoscape.org/apps/ismags. Source code and documentation for ISMAGS are available at https://github.com/biointec/ismags. Source code and documentation for the Cytoscape app are available at https://gitlab.psb.ugent.be/thpar/ISMAGS_Cytoscape.

Supplementary information
Supplementary data are available at Bioinformatics online.
Pathway Inspector: a pathway based web application for RNAseq analysis of model and non-model organisms
Authors: Bianco Luca , Riccadonna Samantha , Lavezzo Enrico , Falda Marco , Formentin Elide , Cavalieri Duccio , Toppo Stefano , Fontana Paolo 
Published: October 2016

Abstract

Summary
Pathway Inspector is an easy-to-use web application helping researchers to find patterns of expression in complex RNAseq experiments. The tool combines two standard approaches for RNAseq analysis: the identification of differentially expressed genes and a topology-based analysis of enriched pathways. Pathway Inspector is equipped with ad hoc interactive graphical interfaces simplifying the discovery of modulated pathways and the integration of the differentially expressed genes in the corresponding pathway topology.

Availability and Implementation
Pathway Inspector is available at the website http://admiral.fmach.it/PI and has been developed in Python, making use of the Django Web Framework.
Flexibility or ethical dilemma: an overview of the work from home policies in modern organizations around the world
Authors: Timsal Ahmad , Awais Mustabsar 
Published: October 2016

Purpose
The primary purpose of this paper is to highlight the pros and cons associated with the work from home policies and how these policies differ across countries and cultures. The main question to be answered is that why a perk or benefit is now being considered as an ethical issue.

Design/methodology/approach
Opinions of practitioners and examples of some leading controversial work from home policies have been discussed in detail. Examples from the developed countries have been compared with those of less developed countries, to present a cross country analysis.

Findings
Culture has a significant impact on the flexible work arrangement policies. Although many companies endorse some degree of flexibility for working mothers or parents in general, working from home as a universal policy is still debatable. The decision to offer this facility to employees majorly depends upon the geographic location of that organization.

Originality/value
All the discussions and views expressed solely belong to the authors. This paper can be extended by adding some empirical evidences from the companies who actually offer this facility to their employees.